Stephen B. Elko, the government's chief prosecution witness in the bribery trial of Rep. Daniel J. Flood (D-Pa.), conceded yesterday that in the past he has lied, obtained money under false pretenses, rifled Flood's files, burned incriminating documents, and contradicted himself in sworn testimony.

Under cross-examination by Flood's lawyer, however, Elko's major assertions which implicated the 16-term congressman in bribery schemes remained largely uncontradicted.

Defense lawyer Axel Kleiboemer's two days of questioning nevertheless elicited an unflattering self-portrait of Elko and a series of admissions that could be damaging to Elko's general credibility with the jury hearing the bribery, conspiracy and perjury charges in U.S. District Court here.

Elko, Flood's former administrative assistant, acknowledged that he stole files from Flood's office and burned some of them after learning he was being investigated.

Though the documents were relevant to the accusations against Flood, Elko said he did it to protect himself, not to impair the congressman's defense.

Elko also acknowledged a number of contradictions between what he has said so far in the Flood trial and what he told federal investigators in the past, though he attributed them to lapses in his memory.

In the trial, for example, he testified that Flood had instructed him to seek a doubling of the bribe money being demanded from a Pennsylvania developer.

In a previous interview with government agents, however, Elko had said he sought the extra money on his own. Asked to explain the contradiction, Elko said yesterday that he changed his story after "I saw more information and refreshed my recollection."

In another instance, Elko at one time told congressional investigators that Flood pocketed one of several $1,000 bribes paid by a New York rabbi seeking a Labor Department grant. In the trial, Elko testified that he took that money himself.

Elko also admitted mistakenly telling earlier interviewers that he used some of the bribe money he took for himself to pay large portions of Flood's living expenses, a contention he has retracted in this trial.

Elko has testified that he served as a conduit over a five-year period for thousands of dollars in bribes paid by businessmen to Flood in exchange for his help in porocuring government grants and contracts.

Flood's lawyers contend that Elko operated the bribery conspiracy on his own, never letting Flood in on it or any of the money.

Elko, who is serving a two-year prison term for bribery and perjury in connection with the case, is testifying here under a grant of immunity.

Elko was calm and undramatic during his testimony, grinning broadly whenever he thought he had scored a point against Flood's lawyers.

In addition to transgressions directly related to the charges, Elko acknowledged others. On one occasion, he said, he obtained $2,500 in cash from a Pennsylvania banker by falsely claiming that Flood's congressional office telephone account was overdrawn and needed replenishing. He said he kept the money for himself.

Prosecution lawyers are expected to call a large number of witnesses over the next three weeks who they hope will corroborate Elko's testimony.

The first such witness appeared late yesterday. Charlotte Fowler, the former executive assistant to Airlie Foundation Director Murdock Head, testified that she had custody of a pool of cash which prosecutors allege was used to bribe Elko and Flood from 1970 to 1974.

She said Dr. Head, whose foundation allgedly sought Flood's help in obtaining grants for its Virginia-based operation, instructed her to inflate business expense account reports to generate the cash.

Usually, she said, she kept between $1,000 and $1,500 in her desk at Head's request, though sometimes as much as $5,000.

"On occasion I was asked [by Head] to clean the money," Fowler testified. "I would put on white gloves and wipe both sides of the money. Then I would put it in a plain white envelope" and deliver it to Head, sometimes further concealed between the pages of a magazine.

She said she never asked Head why she was doing this.