DFA Sec. Alan Peter Cayetano has since apologized to his Kuwaiti counterpart and to the Kuwaiti government who were offended by some actions taken by the embassy officials and personnel.
Kuwait had summoned the Philippine ambassador to demand an explanation.
"The ministry, which also declared recalling the State of Kuwait Ambassador to the Philippines for consultation, said its action against the top Filipino envoy was in retaliation for undiplomatic acts by Philippine embassy staff, encouraging Filipino domestic workers to flee employers' households", the state-run outlet said.
He said that Mr Cayetano had also apologised to Kuwait "for the actions that were undertaken by the embassy ... to assist Filipino nationals in grave distress here in Kuwait but which the government ... found unacceptable".
One clip shows a man rushing to assist a woman into a black vehicle carrying diplomatic licence plates, while another depicted a person running from what looked like a construction site and speeding off in a auto.
A recent video circulated on social media purports to show a Philippines Embassy staffer smuggling domestic workers from Kuwaiti homes into vehicles bearing diplomatic plates.
Kuwait had branded the rescues a violation of its sovereignty, adding fuel to a simmering diplomatic row between the two nations sparked by the murder of a Philippine maid.More news: After Braves waited a month on goal , it's Ronald Acuna Jr
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Domestic helpers account for more than 65 percent of the more than 260,000 Filipinos in Kuwait, according to the Philippines' foreign secretary.
Kuwait's ambassador assured President Rodrigo Duterte late Monday that Filipinos working in Kuwait will be protected, the Department of Foreign Affairs said.
Kuwait was furious after the videos emerged, saying the rescues were a violation of its sovereignty and "can harm relations between the two countries".
In a press conference held at the embassy in Kuwait, the diplomat expressed his country's "gratitude" to the generosity of the Kuwaiti government to more than "250,000 Filipino citizens who consider Kuwait their second home".
About 10 million Filipinos work overseas and the money they send back is a lifeline of the Philippines economy.
The two countries had since been trying to work out an agreement to protect the rights of Filipino workers in Kuwait, particularly some 170,000 maids.