The deputy chief of the Palestine Liberation Organization in Rome was killed today less than a day after another Arab, a PLO sympathizer, was fatally shot here in an ambush.

The PLO office in Rome issued a statement blaming the Israelis for the killings and charging that "terrorist squads of [Prime Minister Menachem] Begin have a free hand in Rome and are trying to annihilate the political cadres of the Palestinian people."

A Israeli Embassy spokesman here denied the charges "completely and categorically" and said they constituted "an appeal for the murder of members of the Israeli Embassy."

Kamal Hussein, 33, a Jordaniann who was deputy chief of the PLO office here, was killed this morning when a shrapnel-loaded car bomb exploded as he drove his car from his garage in an outlying district of Rome. A woman passerby was hurt in the blast.

Late last night, Nazeyk Matar, 32, a Lebanese medical student, journalist and PLO sympathizer was killed by several gumman in an ambush outside his home in a different part of Rome.

Ironically, Hussein had been the first to rush to the scene of Matar's murder, which took place following an anti-Israeli march organized by the PLO and Italian leftists. He had gone there with the Nemer Hammad, the head of the PLO's semiofficial Rome office, in the latter's car. Police speculated that the bomb that killed Hussein was placed around midnight and that both men could have been killed had they taken Hussein's car.

According to the Italian police, this is the first murder of a PLO official in Europe since the Israelis advanced into Lebanon early this month.