But, if NGOs are to be believed the rot would be hard to eliminate through such knee-jerk reactions. They allege that problems in Capart are structural and need to be redressed with a long-term view.
An aspect of the recent blacklisting was that the NGOs were all linked to the agency as early as ten to 15 years ago. "Many of them were fake. When FIRs were lodged against many of them, police found the NGOs did not exist," said Rural Development Minister Raghuvansh Prasad Singh.
NGOs say this just shows the ministry's own incompetence. "The ministry looks at NGOs who had finished their projects 15 years ago and finds that no certificates had been filed. It is possible that the ministry failed to file them. Had it been prompt it would have caught them then,'' said Rajesh Tandon, chief executive officer, NGO, PRIA.
NGOs also question Capart's claim that blacklisted NGOs were fake. "Capart is so inefficient that it does not verify NGOs. How can it give funds to NGOs that don't exist?'' asked Ashok Singh of the NGO network UPVAN in Lucknow.
"It shows a big racket is on in terms of verification of NGOs. It is impossible that NGOs have fake addresses. Where do they send drafts? How do they get drafts?'' he said.
He added that his NGO had asked for a list of the blacklisted NGOs as it was necessary to know who or why they were.
Singh was quick to rise to the defence of his ministry. "We got rid of political nominees heading regional," said Singh.
He added it was often reported that the political nominees gave money to their favourites using fake fronts and the step was successful in stopping this practice.
Bureaucrats, now head the regional panels, which use the Rs 6 crore (Rs 60 million) budget of Capart.
He added that earlier the NGOs were having a field day misusing funds for often fictitious projects like installing hand pumps or building low cost houses for villagers when the central government was running a full fledged programme worth thousands of crore for housing and water, says Singh.
Therefore, the new regime of Capart now disallows contracting of work to outsiders and working on projects which duplicate work being done by various departments
Transparency and openness has been introduced into all dealings between the agency and NGOs by insisting on online aplication by NGOs for sanctioning of projects.
The entire drive to cleanse Capart which many NGOs have criticised as being targeted at them began when Anna Hazare staged a protest a year ago protesting against what he called a corrupt regime in the agency which was not allowing funds for his projects.
The ministry said that in Hazare's village of Ralegav Sidhi, he had 20 projects worth Rs 500 crore (Rs 5 billion), which were in various stages of progress approved by Capart since 1997.
But audit reports were not forthcoming and Hazare had been pressing for release of funds, which the ministry was refusing to do, said ministry officials.
Finally the ministry set up a committee headed by its secretary on the issue. The committee suggested resolution of the issues raised by Anna Hazare on a case-by-case basis, the ministry said.
About 12,000 NGOs have been funded by Capart since its inception in 1986, says MN Kondharkar director of the NGOs' alliance in Maharashtra called Afarm.
The NGOs, which file their audits and funds utilisation reports are also getting letters from the Capart saying that their letters were not received.
He added individuals appointed as monitors by Capart were harassing NGOs and ought to be replaced by institutional monitors. He said that for his own firm, he had sent audits four times but the monitors did not look at them because they are understaffed.
Kondharkar defended Anna Hazare and said that in the Hazare case, Capart rather than Hazare would most likely be in the wrong.