The trade union federation's criticism comes on the back of a statement by fellow ruling party alliance partner, the SA Communist Party (SACP) this week that Molefe was yet to clear his name regarding the damning "State of Capture" report by the Public Protector.
"He still needs to account on why he resigned and when he is responding to allegations [against him] during his term as Eskom CEO," said secretary Bheki Ntshalintshali.
The comments come after Cosatu's three-day central executive committee meeting.
Opposition parties and political commentators claim the controversial appointment of Molefe was based on the removal of MP Abram Mudau, who's constituency was in the North West Province. Mudau has however denied this, saying he resigned because he had been ill for some time.
The SACP and Cosatu slammed the appointment, with the communists saying they were not consulted by its alliance partner, the governing African National Congress (ANC). Ntshalitshali said it had always been consulted on appointments by the ANC, but that this did not happen before Molefe was deployed to Parliament.
"There has never been an appointment of a minister and we were not consulted. Sometimes we're consulted very late, but we are asked for our views...even in the Des van Rooyen appointment issue that caused the rand to fall, we were consulted," he said.
Earlier this month, Cosatu affiliate, the SA Transport and Allied Workers Union (Satawu), said it supported Molefe's appointment and said the former Eskom boss was a capable individual and that Parliament needed "eloquent MPs of his calibre."
Cosatu deputy secretary Solly Phetoe said as part of the executive committee meeting, Satawu leadership were now behind the decision not to support Molefe's appointment.
"Satawu were in the central executive committee meeting...so there was a decision after the matter was discussed. Satawu was there as well and are obviously part of this decision," he said.
Regarding calls by the ANC Youth League and others for Finance Minister Pravin Gordhan to step down, Cosatu said it supported the minister and would not be "personalising issues" at Treasury.
Gordhan's critics accused him of not aligning his budget with the ANC's stance on radical economic transformation.
"There are no clear reasons from those calling for Gordhan to resign, except that his stance was not in line with the State of the Nation Address (SONA)...and those people have not even read the speech," said Ntshalintshali.
"We've been calling Treasury the elephant in the room but we're not personalising issues...people fail to understand that was not Pravin's budget, he took everyone in confidence including ministers. People forget this important issue and choose to go for one individual."