Video of the incident showed Philippine Ambassador to Kuwait Renato Villa, who was reportedly heard as saying that the embassy did not need the aid of Kuwaiti authorities in helping distressed Filipino workers.
In a statement issued Thursday, the Department of Foreign Affairs (DFA) said it also wanted the Kuwaiti government to explain the continued detention of four Filipino drivers hired by the Philippine embassy to help in the rescue, and the issuance of arrest warrants against three diplomatic personnel.
The Foreign Ministry has reiterated its rejection of the embassy's apparent violation of diplomatic norms - specifically the 1961 Vienna Convention on Diplomatic Relations - and "interference in the state's internal affairs and a violation of the work of the state security agencies".
The two states had been working to resolve differences sparked by the murder of a Filipina maid, whose body was found stuffed in her employer's freezer in Kuwait earlier this year.
Talks between the Philippines and Kuwait for a deal on the protection of Filipino migrant workers began following a string of reported abuses and deaths of Philippine workers in the Gulf state, including Joanna Demafelis.
Despite the assurance, the Kuwaiti government declared Villa persona non-grata on Wednesday and gave him one week to leave the country.
"President Rodrigo Duterte and everyone else was shocked at this development because the president's meeting with the Kuwaiti ambassador went well", presidential spokesman Harry Roque said.
Cayateno, however, said Villa will still stay in Kuwait to carry on with assisting our compatriots in need of embassy assistance.
Tensions between the two countries had appeared to cool in recent weeks after the Philippines cemented a ban on its workers being deployed to Kuwait in February over abuse concerns.
Following the verdict, Mr Duterte announced plans to visit Kuwait this month to seal an agreement on workplace safety guarantees for the 252,000 Filipinos already working there.
Some 10 million Filipinos work overseas and the money they remit back is a lifeline of the Philippine economy.