The Commerce Department, taking a new look at the U.S. trade balance with Canada, yesterday lowered last year's merchandise trade deficit with that country by almost $10 billion from the level announced in January.

The new figures place the deficit at $13.3 billion, down from $22.9 billion reported originally. The Commerce Department also reported that the new level represents a $2.4 million decrease from the 1985 deficit of $15.7 billion, the first yearly decline in the U.S. trade deficit with Canada since 1979.

The change resulted from a new agreement between the two countries to do a better job of reconciling their trade figures and was part of a cooperative effort between the U.S. Census Bureau, which collects trade data for the Commerce Department, and Statistics Canada.

The largest adjustment involved $12.7 billion in trade that was not accounted for by export documents that form the basis of the trade figures. According to the reconciliation, $10.2 billion in U.S. sales in Canada and $2.5 billion of Canadian exports to the United States were not counted in the trade figures when they were first compiled.

The new figures were hailed by Canadian Trade Minister Pat Carney, here for meetings with her U.S. counterparts, as a way to ease potential frictions as negotiations for a free trade agreement between the two countries come to a conclusion this summer. The Canadians have complained that Commerce figures overemphasized their trade surplus with the United States because of the large volume of U.S. sales to Canada that were not counted.

The two countries have the largest volume of two-way trade in the world, $124.5 billion last year, but frictions have increased as the United States has run up a series of record trade deficits. The United States is Canada's largest market, accounting for four-fifths of its exports. Canada is also the United States' largest market, but it only accounts for one-fourth of U.S. foreign sales.

The United States has run a trade deficit with Canada every year but one since 1970. But the trade imbalance held steady until 1981, when it jumped to $9.7 billion, and grew to $15.7 billion in 1985.