The party said the two Ministers shouldn't be in office since they were also fingered in the judiciary corruption scandal.
Amaechi is the Minister of Transportation while Onu heads the Science and Technology Ministry.
The party wants President Muhammadu Buhari to suspend the ministers because they were fingered in the ongoing investigations of alleged corrupt judges.
The PDP faction made the call in a statement issued in Abuja on Friday, November 4, by its spokesperson, Dayo Adeyeye.
The party said Buhari should suspend the ministers since the National Judicial Council (NJC) has also suspended the judges involved in the scandal.
Some of the judges - Justices Sylvester Ngwuta and Inyang Okoro had alleged that Amaechi and Onu attempted to influence them to rule on election cases in their favour.
The two judges of the Supreme Court were suspended alongside five others by the NJC on Thursday, November 3.
PDP said: "It is important to note that Justices Ngwuta and Okoro have alleged that they are the targets of a witch hunt because they refused offers of inducement and bribes made to them by the Minister of Transport, Rotimi Amaechi; and the Minister of Science and Technology, Ogbonnaya Onu, to subvert justice in appeals against the decisions of lower courts in election petitions in Abia, Akwa Ibom, Ekiti and Rivers states.
"In order to allow for a fair and independent investigation, it is incumbent on President Muhammadu Buhari to ask these ministers to step aside pending the conclusion of investigations into these issues.
"The judiciary has set a very good example in its quest to fight corruption. It has proved that it is ready to reform itself and we commend the NJC for taking this bold step.
"Anything less will confirm the long-held notion that President Muhammadu Buhari and his administration consider themselves to be above the law and not subject to the provisions of our laws and the institutions of our democracy.
"If President Buhari retains these ministers in the face of the serious allegations against them, he will show that the entire judicial corruption saga is nothing more than a deliberate attempt to blackmail the judiciary in order to subjugate it and make it a rubber stamp institution of the administration."
Other suspended judges are Justice Mohammed Tsamiya (Presiding Justice of the Court of Appeal, Ilorin Division); Justice Kabiru Auta of Kano State High Court; Justice Adeniyi Ademola (Federal High Court, Abuja); Justice I. A. Umezulike, who was a former Chief Judge of Enugu state and Muazu Pindiga of the Federal High Court, Gombe Division.