Three charges against a suspected Lebanese Shiite terrorist accused of hijacking a Jordanian airliner were dismissed here yesterday when a judge ruled that the government lacks jurisdiction to prosecute him for allegedly destroying the plane.

U.S. District Court Judge Barrington D. Parker ruled that Fawaz Younis could be charged with leading the June 11, 1985 hijacking but not with assaulting passengers and blowing up the Royal Jordanian Airline jet at Beirut International Airport.

Parker refused to dismiss six conspiracy and hijacking counts of the indictment and upheld use of Navy vessels that transported Younis after his arrest aboard an FBI-chartered yacht Sept. 13 in the Mediterranean.

Younis, who later told the Federal Bureau of Investigation that Lebanon's justice minister, Nabih Berri, approved the hijacking, was lured aboard the yacht by the prospect of a drug deal, authorities said.

Conviction on the pending hijacking charges could result in life sentences.

Parker ruled that the Aircraft Piracy Act of 1984 provided no jurisdiction for U.S. authorities to prosecute Younis for the bombing of the jetliner. The plane was blown up after the passengers and crew had been released.

The judge ruled, however, that the Justice Department does have jurisdiction to prosecute Younis on the six other charges of conspiracy and hijacking under the Hostage Taking Act, also passed in 1984 as part of a legislative package to combat terrorism.