The man, a taxi driver, went on a leisure cruise to Cyprus three weeks ago, but did not get off the ship after its return to Israel. His belongings remained on board. Following his absence, a complaint was filed wth the Haifa Police.
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Is the underlined part phrasal verb? Is it filled with?
It's "filed with" (not "filled"). If you file a complaint with the police, it means you go into (or phone) the police and tell them that a crime has been committed or that there is some other reason you need to deal with the police.
However, there is a problem with the piece. I understand that the man got on the boat in Israel, but when the ship returned to Israel after its cruise to Cyprus, he was not among the passengers disembarking when it returned to Israel. Three weeks later, a body has been pulled from the water and it is thought to be that of the taxi driver. The problem is with the phrase "After his absence ..." - that makes it sound as if someone like his employer went to the police after he had been absent from work for those three weeks. I think what they mean is "After his disappearance ..." or "After it was realised that he had disappeared ..." "Absent" is not the correct word for these circumstances.