BOSTON (AP) _ A congressman investigating more than 40 break-ins since 1984 at churches and offices of opponents of the Reagan administration's Central American policy says the incidents ''are not common burglaries.''

Rep. Don Edwards, D-Calif., chairman of the subcommittee on civil and constitutional rights, said Tuesday that the panel had begun a preliminary investigation into the break-ins and may hold public hearings this spring.

''We just don't know who's been doing it except there's just too much of a pattern for it to be accidental. These are not common burglaries,'' he said.

Some sanctuary activists, who provide aid and haven for refugees from El Salvador and Guatemala, say they suspect that federal immigration officials are involved in the burglaries. A government spokesman denied the charge.

The sanctuary movement includes about 250 U.S. churches and synagogues.

The latest of the more than 40 break-ins cited by Edwards occurred at a Boston church last weekend. In virtually all the cases, files were rifled and stolen while valuables were left untouched.

Edwards said he had no evidence that any government group or official was involved, but that he was concerned because the FBI had decided not to investigate.

The FBI has said it does not have jurisdiction in the cases, many of which were investigated by local authorities.

The Center for Constitutional Rights, a New York-based civil rights organization, has documented more than 50 incidents of what it calls political harassment since late 1983, including 43 involving sanctuary groups or groups opposed to the Central American policies, said spokesman David Lerner.

Other break-ins have been reported in Cambridge, Washington, D.C., Tucson, Ariz., San Francisco, Los Angeles, and New York, Lerner said.

The government has prosecuted several sanctuary activists for aiding illegal aliens. Sixteen people were indicted as the result of Immigration and Naturalization Service investigations; eight were convicted in May and the rest either pleaded guilty to reduced charges or had charges dropped.

Sanctuary supporters say the aliens are political refugees, but federal officials have said they consider the immigrants economic refugees.

The latest incident, a break-in at the Arlington Street Church in downtown Boston, followed the pattern of the others.

''They smashed all the locks and went into every file drawer,'' said the Rev. Victor Carpenter, senior minister of the 325-member Unitarian-Univ ersalist church. ''They stole nothing. They rifled the files. The sanctuary file itself was taken.''

The break-in came less than 12 hours before Carpenter planned to deliver a sermon titled ''Why We Declared Ourselves a Public Sanctuary,'' which had been advertised on bulletin boards.

The church board of directors voted last month to make the parish a sanctuary, but has housed no refugees yet.

''It is our belief that they wanted to send a message not only to us but to other churches,'' Carpenter said of the break-in, which is being investigated by Boston police.

The Old Cambridge Baptist Church in neighboring Cambridge has been broken into eight times since the fall of 1984, when it became involved in the sanctuary movement, said church administrator Peggy Smith.

Smith and some other sanctuary workers have said they believe immigration officials may be involved.

''Why would the federal government want to break in a place ... when we could go to court and get a search warrant?'' asked Duke Austin, an Immigration and Naturalization Service spokesman in Washington, D.C.

Steve Limon, a Middlesex County assistant district attorney who has been investigating the break-ins in Cambridge for almost a year, said his probe was at ''the end of a dead end.''

Two men were convicted and sentenced in connection with a June break-in, but the other seven cases remain unsolved.

''There really is no direction to go in this case,'' Limon said, noting that all eight break-ins had the same pattern.

''Assuming there is conspiracy, and I'm not saying there is,'' he said, ''It could be a conspiracy on the part of anyone from a government agency to a right-wing or left-wing group and you really don't know where to look because there is no evidence that leads anywhere.''