NICOSIA, Cyprus (AP) _ Libya's official radio today rejected what it called vague charges of terrorism leveled at Libya by Western leaders meeting in Tokyo, and quoted Col. Moammar Khadafy as praising Japanese extremists for ''wrecking'' the Tokyo summit.

The praise from Khadafy apparently was in reference to Sunday's firing of rockets by Japanese terrorists during the summit's opening ceremonies. The rockets missed their target and exploded without hurting anyone.

A Tripoli Radio commentary, monitored in Nicosia, later said ''the summit failed as the Japanese people decided to liberate Tokyo, forcing the heads of state attending the summit to flee from Japan like lizards.''

Today, homemade smoke bombs were planted in a dozen transit stations in Tokyo, and police said they also may have been the work of radicals trying to upset the summit.

The summit was not disrupted by either event.

In a declaration issued Monday in Tokyo the seven leaders pledged counter- measures against ''any state which is clearly involved in sponsoring or supporting international terrorism, and in particular Libya.''

The Tripoli Radio commentary expressed surprise over the stand of those heads of state ''who are not linked to the imperialists crusade against the Arab nation and who have no personal hatred against Khadafy and who are not suffering from a complex like (President) Reagan, the baby killer.''

It did not identify to whom it was referring. Besides Reagan, those attending the conference were the leaders of Britain, France, West Germany, Italy, Canada, Japan, and the Common Market.

The term ''baby killer'' was an apparent reference to the U.S. bombing raid on Libya April 15 in which Libya says Khadafy's 15-month-old daughter was killed.

Both Khadafy's message to the Japanese people and the political commentary were broadcast in Arabic.

The radio said the Khadafy message ''praised the Japanese people's brave revolutionary stand.''

''Leader Khadafy sent a cable of thank to millions of Japanese people following their widespread and popular response to the leader's call to wreck the Tokyo summit and expel baby killers Reagan and Thatcher,'' the broadcast said.

Libya also has labelled Mrs. Thatcher a ''baby killer'' because she permitted British-based U.S. warplanes to be used in the attack on Libya.

The radio said the rocket attack Sunday came shortly after Khadafy urged demonstrations against the summit during an interview on Japanese television.

Protests against the summit ''will result in the expulsion of the American presence from throughout Japan, lead to the trial of the murderers and to the revenge of the Japanese victims of the American atom bombing of Hiroshima and Nagasaki,'' the radio quoted Khadafy's message as saying.