Democratic Alliance Youth leader Mbali Ntuli said the agency's board chairperson Yershen Pillay needed to explain the suspension.
"Reports in the media this morning [Thursday] imply that financial misconduct has taken place at NYDA. NYDA cannot cover up this latest crisis. Young people and the public need answers."
The development agency had consistently wasted state resources on a bloated staffing structure which had no real impact on the lives of young South Africans.
"It remains little more than a deployment vehicle for [ANC] Youth League cadres to access state resources," Ntuli said.
The Inkatha Freedom Party Youth Brigade said the suspension was long overdue. "Mr Ngubeni has run the NYDA to the ground, tattering its image, and denigrating its national identity, credibility and integrity," chairperson Mkhuleko Hlengwa said in a statement.
"During Mr Ngubeni's tenure, the NYDA has been plagued by scandal and chaos," Hlengwa said.
The development agency announced Ngubeni's suspension late on Wednesday. It asked the public and the media to "allow investigations and human resource processes to follow due course".
No reasons were given for the suspension.
Congress of the People Youth said the development agency needed to be disbanded. "The NYDA has become a lost cause and an embarrassment to the cause of the youth in South Africa," spokesperson Bongani Mahlangu said in a statement.
It had become a liability to the government and was failing to address youth problems. It had become a cash cow for the ANC Youth League, which provided most of its staff, he claimed.
The Freedom Front Plus youth said the NYDA should explain the move. "There have already been various allegations of irregularities with regard to Mr Ngubeni in the past three years and it is high time that an investigation is launched," said FF Plus Youth leader Wouter Wessels in a statement.
Since its inception, the development agency had not been functional, but controversial with millions of rand spent on, among other things, festivals, he said.
AfriForum Youth said Ngubeni's suspension was a relief for taxpayers. "The NYDA is not a sustainable organisation, especially if its executives continue to receive exorbitant salaries and bonuses," chairperson Charl Oberholzer said.
"Ngubeni was like a thorn in the flesh that was starting to get infected, but the NYDA kept them in taxpayers' flesh for as long as possible."
Complaints against the NYDA
The NYDA said its deputy executive chairperson Kenny Morolong would serve as acting chief executive officer.
The IFP youth and the FF Plus youth objected to Morolong's appointment.
Wessels said it was unacceptable that Morolong, who was also the North West ANC spokesperson, was appointed.
Hlengwa said Morolong could not be a "referee and player" in running the development agency.
"The fact that Mr Morolong is also a member of the ANC North West provincial executive committee, and also the ANC spokesperson in that province entrenches further the politicisation of the NYDA," he said.
Morolong was not immediately available for comment.
The IFP youth, the FF Plus, Cope Youth and AfriForum have previously laid complaints against the NYDA. – Sapa