A federal judge in Boston set up a major legal roadblock to President Reagan's antiabortion regulations yesterday, and the government announced it would suspend application of new Family Planning Program rules nationwide until the legal situation is clarified.

Federally funded family planning clinics have always been barred from performing abortions. The new rules would also prohibit them from informing a woman that abortion is an option in an unintended pregnancy, or from referring her directly to an outside abortion clinic even if she requests it. These prohibitions were to have gone into effect yesterday.

However, three federal judges have issued injunctions to block the rules as a result of lawsuits brought in Denver by the Planned Parenthood Federation of America, in New York by the State of New York and yesterday in Boston by the state of Massachusetts, the National Family Planning and Reproductive Health Association and the American Public Health Association.

With yesterday's ruling in Boston -- the broadest of the three rulings and the only permanent injunction -- the court orders cover the majority of clinics funded under the program. A Department of Health and Human Services spokesman said regional HHS offices had been notified to take no action to implement the new regulations until the permanent injunction issued by U.S. District Court Judge Walter Jay Skinner in Boston had been studied.

National Family Planning and Reproductive Health Association executive director Scott Swirling said, "The gag rule has been found to be invalid. This will allow continued full information on their medical options to be made known to millions of low-income women around the country."

In issuing his injunction, Skinner said it applied to all members of the plaintiff groups nationwide. The proposed rules, Skinner said, would "as a whole violate both congressional intent and rights protected by the Constitution . . . . In my opinion, a governmentally imposed block on the flow of neutral information bearing on abortion is an impermissible burden on the presently recognized rights of a pregnant client."

Swirling estimated that at least two-thirds of all federally funded clinics are affiliated with his group and would be covered by the ruling.

In the Denver case, U.S. District Court Judge Zita Weinshienk issued a preliminary injunction, pending a decision on the merits, against application of the new federal rules to any Planned Parenthood clinics around the nation. The New York ruling, also a preliminary decision pending further litigation, applied only to that state.

In all three cases, the administration is expected to challenge the rulings or contest the case on the merits. The administration and antiabortion groups such as the National Right to Life Committee have argued that existing rules, calling for clinics to inform women that abortion is an option, have the effect of fostering abortion, which the law does not allow.

Under the $137 million annual family planning grant progam, authorized in 1970, the federal government makes grants to local family planning clinics to provide services to low-income women, including both contraception and fertility services. From four million to five million low-income women and teen-agers receive services.