The Federal Trade Commission decided yesterday to press on with its controversial inquiry into television advertising aimed at children, despite the court-ordered disqualification of Chairman Michael Pertschuk.

After U.S. District Judge Gerhard A. Gesell ruled two weeks ago that Pertschuk could not participate in the proceeding because he had shown bias, a number of groups with a financial stake in children's advertising asked the commission to abandon the proceeding and to start again. The request was made to remove the "taint" resulting from Pertschuk's participation.

The FTC said yesterday that Gesell's ruling did not require it to take such an action and announced its intention to proceed on schedule. The agency also said it found no reason to grant a motion to remove the presiding officer, Morton Needelman.

In a related development, Gesell yesterday upheld the basic rules of the proceeding and rejected a request by the Kellogg Co. that he order the rulemaking started again from the beginning.

The deadline for public comment remains Nov. 24, and hearings are scheduled to begin in January in San Francisco on a variety of FTC staff proposals to regulate children's advertising, the FTC noted. The staff proposals include:

A ban of all TV commercials aimed at children "too young" to understand the selling purposes of advertising.

A ban on the advertising of highly sugared products to children under the age of 12.

A requirement that advertisers of other sugared products aimed at youngsters contribute to a fund that would balance the ads with separate dental and nutrition messages.

The FTC votes yesterday were unanimous, with Pertschuk and Commissioner Robert Pitofsky not participating. Pitofsky, the newest member of the commission, is not participating because, as a professor at Georgetown law school, he served as chairman of the board of directors of a public interest law group representing one of the two parties that petitioned the FTC to initiate the proceeding.

The FTC has not yet taken up the question of whether to appeal Gesell's disqualification of Pertschuk. An appeal would have to be made within 60 days of the ruling.