The chief judge of the U.S. Dstrict Court here yesterday refused to dismiss a conspiracy indictment against former FBI director L. Patrick Gray III, whose lawyer had argued that the government's evidence no longer supported the charge against Gray.

In a brief opinion, Chief Judge William B. Bryant said that there was "no doubt that the exhaustive and admirable investigation" by Gray's lawyer, Alan L. Baron, "revealed certain weaknesses in the case the government presented to the grand jury" 2 1/2 years ago.

Gray and two former top FBI officials were indicted for allegedly authorizing warrantless searches in connection with the bureau's pursuit of fugitive members of the Weather Underground organization in the early 1970s.

But Bryant said he was convinced that the factual gaps attributed to the prosecutors "reflect an honest, albeit imperfect, attempt to recreate past events," and do not warrant dismissal of the indictment.

"Mr. Gray will have an opportunity at trial to set the record straight," Bryant said.

He noted that the government "virtually concedes" the results of Baron's investigation: that Gray did not give top FBI men authorization to conduct the break-ins at a meeting in 1972 and that surreptitious entries without warrants, known as black-bag jobs, had occurred before Gray became director. The government, however, maintains that it still has a criminal case against Gray.

Bryant said there was no information that the prosecutor knew the facts uncovered by Gray's lawyer at the time of indictment, and that there was no evidence of the "serious prosecutorial misconduct" that would be traditionally needed to support dismissal of the indictment.

Meanwhile, government prosecutors yesterday continued the presentation of their case in federal court against W. Mark Felt, the former No. 2 man at the bureau, and Edward S. Miller, who was the head of the bureau's domestic intelligence division.

Felt and Miller were indicted with Gray, but as being tried separately as co-defendants.

Most of the court proceedings yesterday, in which Bryant is also presiding, were taken up with disputes, outside the presence of the jury, concerning the government's use of certain documentary evidence in the case.