Congress completed action yesterday on a bill to increase fees for filing and maintaining patents, but raising them less than President Reagan had proposed in his fiscal 1983 budget.

The administration proposal would have increased the cost of filing, issuing and maintaining a patent from 50 percent of the application processing costs to 100 percent, or at least $3,200, beginning Oct. 1.

Instead, the bill passed by the Senate yesterday would establish a two-tier payment system. Large firms still would have to pay the amount proposed by the president, but small firms, independent inventors and non-profit organizations would pay only 50 percent, or $1,600.

The two-tier approach is expected to produce $7 million less for the Patent and Trademark Office than the president's proposal.

The administration had sought to increase the fees as part of its effort to have users of federal services pay their full cost.

Others were concerned about the impact. Sen. Lowell P. Weicker (R-Conn.), who sponsored the Senate bill, said, "While these costs are not likely to pose a significant financial burden for large firms, I am concerned that they would have a severe chilling effect on those who have demonstrated to be the most innovative, job-producing sectors of our economy--small business and independent inventors."

The bill, which passed the House in June, now goes to the president.