The U.S. merchandise trade deficit surged to its highest level in history in September, $15.5 billion, with the greatest deficit coming in the manufacturing sector where this country maintained a surplus as recently as 1981, the Commerce Department reported yesterday.

Commerce Secretary Malcolm Baldrige called the trade problem "serious" and predicted no letup in soaring deficits until mid-1986. Some economists said continued high trade deficits would hold back the economy, already sluggish, in the fourth quarter of this year.

David Berson, senior economist with Wharton Econometrics Forecasting Associates, said the nation's economic growth is likely to fall to 2.2 percent in the final quarter after running at a 3.3 percent rate in the summer.

One sign of how imports are hurting the economy was a separate Commerce Department report yesterday showing that factory orders dipped 0.6 percent in September. During that month, imports increased 13.7 percent, to $33.3 billion.

Senate Democrats, blaming the trade deficit for the loss of 340,000 manufacturing jobs since January and factory closings throughout the country, immediately intensified their pressure for tougher trade laws. "The president's inaction is going to cause Congress to act," said Sen. Max Baucus (D-Mont.), angry because Reagan has refused to limit copper imports.

Sen. George J. Mitchell (D-Maine) called the trade figures "just plain scary," while Sen. Lloyd Bentsen (D-Tex.) said, "the deficit is up, imports are up, and that certainly doesn't do our economy any good."

But Baldrige called the $15.5 billion September trade deficit a statistical aberration caused by "a good deal of under-reporting in the summer -- July and August -- that was picked up in September." July and August figures showed a surprising fall off in the trade deficit -- to $10.5 billion and $9.9 billion -- which some economists saw as the beginning of a turnaround. That optimism appears now to have been premature.

The previous monthly high trade deficit was $13.7 billion set in July 1984.

"You can expect to see more ups and downs in the monthly trade deficits before you see the start of a sustained decline," Baldrige said in a speech to the National Press Club. "I really think the trade deficit will begin to decline next year . . . the middle of next year."

He said Reagan's aggressive new attack on the trade deficit, launched in September amid a bipartisan firestorm of protectionist pressures in Congress, will lead to an improved U.S. trade picture. Baldrige especially cited coordinated efforts with Japan, Britain, France and Germany to bring down the overvalued dollar, which he blamed for half of the trade deficit, expected to reach $150 billion this year.

Nonetheless, Commerce Department chief economist Robert Ortner pointed out that $15 billion "used to be a rather large deficit for a whole year. I'm not sure we've seen the last of those records."

The release of the trade figures prompted an announcement from U.S. Trade Representative Clayton Yeutter of an embargo on imports for the rest of the year on certain categories of steel from America's closest allies in Western Europe.

Yeutter called a 20.9 percent increase in EC steel imports this year "an unconscionable violation of the spirit" of a 1982 agreement and said the community faces "import levels far below current shipments" unless a new pact is reached by today. Sir Roy Denman, EC ambassador to the United States, said, however, that the two sides "are close to an agreement" in negotiations taking place in Brussels.

The trade deficit in manufactured goods in September totaled $12.2 billion, which is about the same figure as the nation's all-time surplus in manufactured products, $12.5 billion, posted just five years ago.

Other countries shipped $24.4 billion worth of manufactured goods to the United States in September, including $4 billion in new cars, $1.7 billion in telecommunications equipment, $1.7 billion in electrical machinery, $1.5 billion in clothing, $1.1 billion in iron and steel products, $1.1 billion in office machines and data processing equipment, $1 billion in auto parts, $800 million in power generators and $800 million in industrial machines.

Car shipments from Japan alone rose to $2 billion in September, up from $1.7 billion the previous month. Japan continued to hold the largest surplus of any nation with the United States -- responsible for more than one-third of the entire $106.7 billion nine-month deficit and posting a record $5.1 billion surplus in September.

While the United States was running up record trade deficits, the Japanese government announced in Tokyo yesterday a record trade surplus for the first half of its current fiscal year.