The nation's merchandise trade deficit, calculated for the first time to include the cost of insurance and freight, increased from $4.07 billion in December to $4.76 billion in January, the Commerce Department reported yesterday.

Under a provision of the trade bill approved by Congress last year, the Commerce Department now must report imports initially with the cost of freight and insurance included (C.I.F. basis). The department then must wait another 48 hours, under the law, before it can issue the traditional merchanside trade report without the extra costs. That report will be available Monday.

The new requirement, under present circumstances, causes the trade deficit to appear larger, the apparent intent of the sponsor of the provision, Senate Finance Committee Chairman Russell B. Long (D-La.)

The deficit calculated with imports valued at cost, not including insurance and freight, probably was about $1.2 billion less, but the increase from December to January on this basis likely was still in the neighborhood of $700 million, private analysts said.

The increase in the deficit was not due to a jump in the cost of oil imports, for a change Imports of petroleum and related products declined 4 percent in January to $6.48 billion from $6.75 billion the month before, on the C.I.F. basis, the department said.

Rather, there was a general 6.2 percent increase in imports while exports rose only 3.6 percent. Much of the change was due to a $400 million drop in agricultural exports and a $1.6 billion surge in imports for manufactured goods. Exports of manufactured goods rose only $450 million.

Insurance and freight, while they must be paid by an importer as part of the total cost of the goods he buys, are not regarded by trade specialists as part of merchandise trade. They are considered as services, and as such are part of a very different picture of the international transactions of the United States.

The United States has had a merchandise trade deficit, even with imports counted on the old (F.A.S.) basis, every month since May 1976. But over the same period of time, the United States has had a growing surplus in service transactions and other items that are included in what is known as the balance of current account. Those other items include earnings of U.S. investments abroad, royalties, tourism, personal remittances and the like.

Since it is impossible to calculate exports on a C.I.F. basis, and since most exports are not carried by U.S. ships, many analysts perfer to compare exports and imports without reference to insurance and freight charges.

Nevertheless, Long insisted last year on adding a provision to the legislation implementing the results of the new multilateral trade pact concluded last year to restrict use of import data without the extra charges. No hearings or debate on the provision took place, but it was generally assumed by government statisticians at the time that Long simply wanted to inflate the apparent U.S. trade deficit to make it easier to pass protectionist bills in the future.

The Carter administration opposed the provision but was forced to accept it as part of the trade package which was brought to the floor just for an up or down vote with no amendments permitted.

Earlier this week Commerce Department officials held a special briefing for reporters to explain the new restriction. They said they were concerned that some people, including traders on foreign exchange markets, might be misled by an inappropriate comparison between a December deficit counting imports on the old basis and a January deficit with them on a C.I.F. basis.

Even with merchandise trade in deficit to the tune of more than $37 billon last year, with imports on a C.I.F. basis, the overall balance on current account was probably narrowly in surplus, administration officials believe. Final current account figures for 1979 will be released next month.

Despite a huge increase in the U.S. oil import bill, the administration expects the current account to remain close to balance in 1980.