The fairly new practice of broad-casting independent television stations signals over cable linkups to millions of homes around the nation may pose "a serious challenge" to general non-network television programming, a Commerce Department official warned yesterday.

In a speech before a conference of the Association of Independent Television Stations here, Deputy Assistant Secretary for Communications and Information Paul Bortz suggested that unlimited importation of outside independent programming by cable operaters might undercut local program development.

In an apparent drift from the administration stance calling for a decrease in regulation of the airwaves, Bortz said the growth of "super stations" -- independent local stations that are retransmitted without compensation around the nation -- "intensifies the problem" of a shrinking local programming market.

Congress and the Carter administration are working on proposals to dramatically revamp regulation of the communications industry, including major changes in the cable television market.

Some entrepreneurs owning independent stations, including Ted Turner of Atlanta, have already taken advantage of cable television nation-wide exposure to charge special advertising rates based upon the number of viewers locally and nationally.

But Bortz is concerned that local stations which may have, for example, purchased local rights to transmit certain movies will be unfairly undercut by a cable transmission of an out-of-town independent station showing the same movie.

Bortz pointed out other inconsistencies involving sports blackouts and copyright infringement laws.

"Clearly," he said, "such a game could not have been devised following any rational process which considered the rights of all four players: The copyright owner; the cable owner; the broadcaster; and the common carrier."