Accused spy Jerry Alfred Whitworth pleaded not guilty yesterday in federal court in San Francisco to new charges that he stole Navy technical manuals and design plans for code machines for sale to the Soviets by the Walker family espionage ring.

Whitworth, 46, a retired Navy communications specialist, entered the plea during a four-minute arraignment before U.S. Magistrate Wayne Brazil. The latest charges were contained in a new indictment returned Tuesday.

Whitworth, who is being held without bond, did not speak during the brief hearing, except to say that he had read the indictment, the fourth returned against him in the case.

According to a source familiar with the case, the fresh allegations are based on recent statements to FBI agents by John Anthony Walker Jr., the ring's admitted leader, who pleaded guilty to espionage Oct. 28 in Baltimore and agreed to cooperate with investigators.

Assistant U.S. Attorney William Farmer declined to comment yesterday on Walker's cooperation, but said the charges were based on information "not previously available to the grand jury."

Whitworth was charged earlier with providing Walker with "key lists" and "key cards" that were changed daily in the process of encoding and decoding classified Navy messages. Possession of the manuals and design plans as well would have allowed the Soviets to read secret Navy communications, sources said.

Tony Tamburello, a lawyer defending Whitworth, has attacked the new charges as based on information supplied by a convicted felon, Walker, and therefore untrustworthy.

The two sides are scheduled to appear in court again on Monday as a hearing continues on whether statements by Whitworth and evidence gathered during searches of his Davis, Calif., mobile home last May should be suppressed. Whitworth testified last Friday that he gave permission for the searches and made the statements while under duress.

Whitworth, a retired senior chief radioman, allegedly received a total of $332,000 from Walker for classified materials, which he is charged with turning over in a series of clandestine meetings with Walker in California, Hong Kong and Manila from August 1977 to June 1983.

Besides several espionage counts, Whitworth is charged with evading income tax on the alleged payments from Walker. Trial is scheduled to begin Jan. 13.