Johor crown prince Tunku Ismail Sultan Ibrahim claimed that Putrajaya failed to consult the conference of rulers when it decided to accede to the Rome Statute.
"I was told by his majesty DYMM Tuanku that the rulers were never consulted.
"If this was the case, you have undermined the conference of rulers," he said in a Twitter posting tonight.
Wisma Putra had previously stated that the matter was presented to the Yang di-Pertuan Agong.
The Rome Statute governs the International Criminal Court (ICC) which tries four core international crimes, namely genocide, crimes against humanity, war crimes and crime of aggression.
On Friday, Tunku Ismail had also claimed that Malaysia's move to accede to the Rome Statute would render the Malay rulers irrelevant and impact the status of Malays and Islam in Malaysia.
This prompted Wisma Putra to earlier today assure that the position of the Yang di-Pertuan Agong would not be compromised.
Wisma Putra, in its statement, said Prime Minister Dr Mahathir Mohamad had written to then acting Yang di-Pertuan Agong Sultan Nazrin Shah about the Rome Statute on Dec 26, 2018.
Subsequently, it said Foreign Minister Saifuddin Abdullah again presented an explanation on the matter to Sultan Abdullah Sultan Ahmad Shah on Feb 15.
It added that as of March 4, 124 countries are party to the Rome Statute.
These countries include constitutional monarchies such as Belgium, Cambodia, Denmark, Japan, Jordan, Lesotho, Liechtenstein, Luxembourg, Netherlands, Norway, Samoa, Spain, Sweden and the United Kingdom.
Tunku Ismail in a separate Facebook post tonight, claimed Putrajaya's move to accede to the Rome Statute was "not good" for the rulers, Malays and Islam.
"The Rome Statute of the ICC was created by the United Nations. Who benefits from it? Only a handful of superpowers. How come they never question what is happening to the Palestinians and how they are suffering?
"This is not good for the Rulers, Malays and Islam. Without you realising, we Malays, are making it easier to fall into their trap and agenda. This is the price we pay for wanting to be too liberal. Always uphold Islam," he said.
Tunku Ismail claimed the treaty puts the Yang di-Pertuan Agong, who is also the commander in chief, in a precarious position of being liable and be dragged to the international court.
"Decisions affecting the commander in chief must first obtain consent from the conference of rulers," he said.
Malaysia acceding to the Rome Statute was announced on Tuesday.