WASHINGTON, July 22— The Washington Times, the capital's unabashedly conservative ''other paper,'' is once again the unwelcome subject of articles on its own front page.

The man who, until two weeks ago, was The Washington Times's top executive has charged that the newspaper has fallen under the editorial control of the Unification Church, which is headed by the Rev. Sun Myung Moon. The allegations add fuel to a controversy that has dogged the paper since its inception two and a half years ago.

As the self-proclaimed conservative alternative to The Washington Post, the newspaper has fought an uphill battle to convince readers that it is an independent news source despite its ownership by News World Communications, the publishing arm of Mr. Moon's movement.

Until recently no one was a more vigorous exponent of the view that the newspaper was independent than James Whelan, its founding publisher and editor. Mr. Whelan was responsible for planning and developing the newspaper, as well as for directing its business and editorial operations, until July 12, when he was relieved of his duties in what Washington Times officials say was a dispute over his salary. Smith Hempstone, the executive editor, was then named editor in chief. Dispute Over Independence

But Mr. Whelan says the dispute involved the paper's independence. In the past week he has become the newspaper's most vocal critic, charging that his ouster was a power play by the Unification Church elders and evidence that The Times has become what detractors have always asserted, ''a Moonie newspaper.''

The dispute between Mr. Whelan and his former employers has resulted in charges and countercharges, aired for the most part on the front pages of The Washington Times and The Washington Post.

Times news executives, none of whom are members of the Unification Church, have vehemently denied Mr. Whelan's accusations. They released copies of Mr. Whelan's contract demands and a new statement of editorial policy issued by News World Communications reiterating a commitment to the integrity and autonomy of the paper's editorial and news departments.

According to the proposed five-year contract, Mr. Whelan, who is 50 years old, sought increases that would have brought his $90,000 annual salary to $185,000 by 1989, replacement of his company-provided Cadillac every 40,000 miles, paid membership in four private clubs and a country club, and new financial arrangements for his company-owned residence. Letter from Executives

The newspaper also made public a letter signed by six top executives stating that the newspaper's welfare required Mr. Whelan's replacement as editor and publisher. ''We do not feel it is in the best interest of The Washington Times for James R. Whelan to continue to hold these positions,'' the statement said.

Mr. Whelan has countered by saying he had renounced his salary and benefit demands before his removal and that the true bone of contention was his insistence on sufficient independence from Col. Bo Hi Pak, chairman of News World Communications and a close associate of Mr. Moon.

Neither Mr. Whelan nor his attorney could be reached for comment today.

In a July 18 letter to The Washington Post released Friday by Mr. Whelan, he said, ''I had no intention ever of impugning the motives of those who, until a few days ago, were my close associates and who, until they realized I was going public, were together with the owners, unstinting in their praise of me.''

Mr. Whelan said he had watched in shock as his former colleagues engaged ''in the vilest form of character assassination, dredging up every resentment - every grievance, every grudge, real or imaginary - all for the sole and single purpose of disguising the fact that they had gone along with what they had said they would never go along with: direct Moonie control of The Washington Times. '' A 'Compact of Trust'

The former publisher said he bore no malice against The Times or its staff. ''But I could not stand by, either, and do nothing while a compact of trust was turned to ashes,'' he said. ''That is why I have fought.'' The newspaper, which has few advertisements, has an estimated paid circulation of 95,000, while The Washington Post has a daily total of almost 719,000. But The Times is influential in the capital among conservatives and is often quoted by President Reagan.

News World Communications has pumped $150 million into The Washington Times so far. Despite its estimates that the newspaper will not break even for five years, the company has begun printing a nationwide edition on the West Coast and plans to start printing in Chicago and Dallas later this year. The newspaper has also announced plans to open about a dozen foreign news bureaus. Difficulties in Recruitment

The 240 newsroom employees at The Times include in key positions about 30 veteran reporters and editors who worked at The Washington Star before that highly regarded afternoon daily closed in August 1981.

Editors at The Times acknowledge that the financial link to Mr. Moon posed recruitment problems in the newspaper's early days, when rumors were rife that newsroom jobs would be filled with inexperienced church followers who would be groomed to take over responsible positions.

Recalling the recruiting problems, the associate editor, Coyt Hendley Jr., who had been an editor at The Washington Star, said: ''Everyone asked the same question: 'Why should I come to work for a Moonie newspaper?' I asked it myself.''

He said about 30 of the paper's editorial employees were Unification Church members, but only two of them occupy senior positions. Mr. Hendley and others at The Times insist that there has been no interference in editorial operations.

Conscious of the mistrust that surrounds its relationship to the church, The Times takes great care in handling coverage of articles involving Mr. Moon or church activities. In an effort to avoid charges of bias, the newspaper used a wire-service report for its front-page article on Mr. Moon's conviction of tax fraud, and according to one senior editor it agonized for many months before running an editorial in support of Mr. Moon's position. Dozens of religious and civil liberty groups had also taken Mr. Moon's side in the case.

Jeremiah O'Leary, the White House correspondent for The Times, who was a 45-year veteran of the Washington Star, said he had never detected any tampering with his articles.

Mr. Hendley and Mr. O'Leary praised Mr. Whelan for his contributions to The Times, but both described the staff as jubilant at his departure.

Mr. O'Leary said most staff members felt betrayed by Mr. Whelan's charges of church interference. ''Whelan tried to pull all of us down with him,'' Mr. O'Leary said. ''There is not a much bigger torpedo you can fire at a paper that has been fighting the Moonie image for the past two years.''

photo of James Whelan