European Common Market governments decided yesterday to withdraw their top diplomats from Iran to protest Ayatollah Ruhollan Khomeini's renewed order for Moslems to kill novelist Salman Rushdie. Britain went further by pulling out its entire embassy staff.

Foreign Secretary Sir Geoffrey Howe said the death threats against Rushdie and the publishers of The Satanic Verses for allegedly blaspheming Islam were "unwarranted interference" in Britain's internal affairs.

He left open the possibility of expelling Iran's lone diplomat in London, where Rushdie lives.

The 12 European Economic Community governments, in a sharp blow to Iran's hopes of improving relations with Western nations, decided to recall their diplomats for consultations and suspend high-level visits to and from Iran.

They said they also will restrict the movement of Iranian diplomats in their countries.

Howe told a news conference that the EEC foreign ministers, meeting in Brussels, had sent "a strong, concerted signal to the Iranian leadership that Khomeini's threats are an affront to international standards of behavior and will not be tolerated."

For Britain's part, he said, "it is no longer sensible to maintain a diplomatic presence in Tehran."

Iran's charge d'affaires in London, Mohammad Basti, will be summoned to hear "the reasons for this action along with the implications for Mr. Basti and his mission," Howe said.

Asked if that meant closing the Iranian Embassy, he replied, "I leave it for your own conclusions."

Rushdie, 41, apologized Saturday for any distress the publication of his book caused to Moslems, after Iranian President Ali Khamanei indicated that could lead to a pardon.

On Sunday, however, Iran's official Islamic Republic News Agency quoted Khomeini as ruling out any reprieve for Rushdie and urging Moslems to "send him to hell" for his writings.

Neither Khomeini's statement nor IRNA referred to Khamanei's comments, reflecting a widening rift in the Iranian hierarchy over the Rushdie affair.

"There plainly is confusion amongst the Iran authorities," Howe said.

He added, however, "If the threat were turned into fact, that would call for an even more serious response, but I hope that it will not come to that."

Iran's deputy parliament speaker, Mehdi Karrubi, reaffirmed Khomeini's execution order Monday, IRNA reported.

Rushdie, an Indian-born Moslem, has been in hiding, reportedly under armed police guard, since Khomeini decreed February 14 that he should be killed, and two Iranian religious leaders put a $5.2 million bounty on his head.