A stopgap funding resolution to carry the government into the new fiscal year hit a snag in the Senate last night, raising doubts whether Congress can pass it in time to avoid the disruption of government activities Friday.

Although Congress still has time to finish the measure, so many amendments were pending in the Senate when it quit for the night that Appropriations Committee Chairman Mark O. Hatfield (R-Ore.) said it would be impossible to consider them all and still meet the midnight Thursday deadline.

That was true even though at least one controversial provision, to strip the Federal Trade Commission of authority over doctors and other members of state-regulated professions, was laid aside in hopes of speeding passage of the spending measure.

Congress' problem is that it has yet to pass any appropriations bills for the new fiscal year starting Friday, and current spending authority for all government agencies runs out at midnight Thursday.

Congress frequently goes down to the wire on interim spending bills but muddles through in the end, causing only minor disruptions in the government. However, last year the government was shut down for a day when Congress and President Reagan deadlocked over stopgap spending authority and the deadline was missed.

This time congressional leaders believe they can avoid a veto if a satisfactory compromise can be reached with Reagan on defense spending levels. The more immediate problem is a glut of proposed Senate amendments -- at least 40 by early evening -- that included some so controversial that senators refused to give unanimous consent to move ahead with the bill in advance of its normal schedule.

Among them was a proposal from Sen. Jesse Helms (R-N.C.) to prohibit use of compulsory union dues for political action committees, which Democrats were strongly opposing. Another would cut off funding for the controversial Clinch River nuclear breeder reactor.

The bill can come up in routine fashion early today, but Hatfield said it is "not conceivable under any circumstances" that the bill could be finished by midnight Thursday unless many of the amendments are withdrawn. "I think it makes it impossible to meet the deadline if the proponents of amendments pursue them," he said.

Senate leaders kept up pressure last night on their colleagues to withhold amendments, but it was not clear whether they would succeed. Sen James A. McClure (R-Idaho) rose early in the discussion to say he would pull back the FTC proposal after being assured that the jurisdiction issue will be considered in the scheduled lame-duck session after the November elections, but he started no stampede.

At one point, Senate Majority Leader Howard H. Baker Jr. (R-Tenn.) complained that, even as he took the floor to beg his colleagues to hold back on amendments, seven more amendments were added to the pile. Staying in session last night might do more harm than good, he added, noting that "amendments are like mushrooms: they grow after dark."

Earlier, the Senate approved a $27.4 billion agriculture appropriations bill that restores $2 billion in spending that Reagan wanted to cut from food stamp and other nutrition programs. The bill was also amended on the floor to include several funding increases sought by farmers, including $600 million in emergency loans and deferred repayment of delinquent loans when farmers have demonstrated good management practices.

The measure now goes to conference with the House, which has approved a bill that meets Reagan's spending targets but does so by several devices, including less than full-year funding for food stamps and other major nutrition programs.