Villa was summoned twice, KUNA's report said, to receive Kuwait's complaints about the "dangerous transgressions" and the request for the embassy to provide within three months the names of Filipinos who had committed the offense of smuggling Filipina workers.
Official news agency KUNA said the Philippine ambassador had been given a week to leave, amid a diplomatic row between the two nations sparked by the murder of a Filipina maid in the oil-rich state.
Foreign Affairs Secretary Alan Peter Cayetano said Kuwait has accepted the Philippines' explanation after the Kuwaiti ambassador met President Rodrigo Duterte on Monday in southern Davao city and held talks with Cayetano on Tuesday in Manila.
"The DFA takes responsibility, I myself have not only assured the president that we're doing what we can for the overseas Filipino workers but have apologised na nangyari but like the Kuwaitis, the president understands na life or death", he said.
"We're sending a note now to my counterpart, and we are apologising for certain incidents that Kuwait views as violation of their sovereignty", Cayetano told reporters.
Joanna Demafelis went missing in September 2016, and her body was found on February 6 in a freezer in an abandoned apartment in Kuwait City, where it had reportedly been kept for more than a year.
He also said the DFA took "responsibility" for what happened after after the Kuwaiti embassy issued two diplomatic protests about the operations. The employers did not hand over their passports.More news: We are on frontier of massive change, says Kanye
Duterte's spokesman Harry Roque said part of an agreement with Kuwait was to seek assurance it would to bring those who abused Filipino workers to justice.
Some workers were persuaded to leave their employers, he said.
Kuwaiti officials said the actions of the Filipino embassy staff violated tenants of the "Vienna convention and amounted to abuses of Kuwait's sovereignty".
"It was not a clandestine operation", said Elmer Cato, Philippine assistant secretary for public diplomacy, according to Reuters.
However, Kuwaitis welcomed the expulsion as a correct measure, with conservative lawmaker Shuaib al-Muwaizri saying the decision should not be revised.
Cayetano also stressed the importance of listening to the concerns of the Kuwaiti government before signing the bilateral agreement between the Philippines and Kuwait and also before lifting the total ban on employment of OFWs in the Gulf state.
"The Ministry of Foreign Affairs should not accept any offers made by the Philippines president or his foreign affairs secretary", Muwaizri said in a message posted on Twitter.