CIA employes have been taking classified documents home with them in "flagrant and deliberate violation" of the agency's security rules for a long time, a Federal court jury was told here yesterday.

Defense lawyers for spy suspect William P. Kampiles emphasized the lax practices in U.S. District Court here where Kampiles is standing trial on espionage charges. He is accused of having stolen a top secret spy satellite manual while he was a CIA employ and then selling it to a Soviet agent on a trip to Athens last winter.

Kampiles has pleaded not guilty, insisting that he "conned" $3,000 from a Soviet military attache named Michael Zavali by simply pretending to let the Russians enlist him.

With a CIA official on the witness stand, Kampiles' defense lawyer, Michael Monico, tried to suggest to the jurors that the document he is accused of peddling - a red-and-white technical manual on the Kmll spy satellite - may have been removed by someone else or possibly destroyed.

The witness, Kevin Donoghue, a deputy chief in the CIA Operations Center where Kampiles once worked, acknowledged that he himself had destroyed an early edition of the Kmll manual in December of 1976 without following CIA rules calling for the presence of two witnesses.

"What if you'd been accused of taking that document home and you couldn't produce it?" You'd have a difficult time proving you didn't, wouldn't you?" Monico asked him.

"Yes, I would," Donoghue conceded. He acknowledged that CIA Director Stansfield Turner sent a memorandum to agency officials July 11 of this year complaining that "many employes are removing agency documents from their office environments and taking them home for work-related purposes."

"This practice," the Stansfield continued, "is a flagrant and deliberate violation of agency security regulations and must be stopped immediately."

Special passes are now required for parcels carried out of CIA headquarters.

The CIA did not realize one of the operations center's three copies of the K11 technical manual was missing until FBI agents extracted a confession from Kampiles on Aug. 15, a confession he is now contending was "coerced."

Donoghue was the CIA official in charge of the three copies the operations center received in December 1976 replacing the earlier edition which he said he burned. Donoghue said two were kept on the sixth floor where he worked, while one was sent upstairs where watch officers such as Kampiles were employed.

The government contends it is that copy, No. 155, that Kampiles hid under his sports jacket and later sold to the Soviet Union.

Donoghue conducted the CIA's search for No. 155 on Aug. 17, the same day FBI agents arrested Kampiles at his apartment in Munster, Ind. The CIA official said he looked in file cabinets, desks and drawers in the 7th floor operations center suite. However, under cross-examination, Donoghue said he did not ask anyone who worked there when they had last seen the document.

There have been suggestions from former CIA officials that junior officers such as Kampiles never should have had access to such documents. But Donoghue said that watch officers in the operations center needed the manual to know whether the satellite could supply required photographs for their part of the world.

In its fourth day, the trial also produced some insights into CIA personnel practices. Paul Corscadden, a former deputy director of the operations center, said he told the 23-year-old Kampiles in the late spring of 1977 and again in late summer that there had been "some rather unfavorable comments" about him from fellow employes and improvement was needed.

Defense lawyer Monico charged that Kampiles had been held to account primarily for extracurricular activities, such as advances he was said to have made during a party to two young women who worked in the operations center. Corscadden denied passing that story on to FBI agents last month, but he said he did tell them of one question Kampiles had reportedly asked another CIA employee about his recent sexual successes.

"So you remember that?" Monico demanded.

"It was part of the legend of Bill Kampiles," Corscadden replied.