The first of the two deputy directors to have been reappointed alongside Ringera stepped down earlier this month.
Members of parliament, who are on recess until November 10, had been threatening to hold up government spending bills over the row, but the resignations will diffuse the potential clash between Kibaki and parliament.
Anti-corruption activists, however, said that Wednesday's move failed to address the fundamental problems within the commission.
"I don't see anything changing in this situation, barring changes in the law"
"The anti-corruption commission is a very weak institution, in a very corrupt environment and where there is impunity," Mwalimu Mati of the Mars Group for leadership, governance and accountability said.
"I don't see anything changing in this situation, barring changes in the law."
In a speech on Wednesday, Ringera rejected the accusations that his office had been inactive.
He said the commission had investigated and recommended the prosecution of eight government ministers, four members of parliament, 11 permanent secretaries and 65 directors or chief executive officers of public institutions.
Kenya has been ranked by Transparency International as the most corrupt nation in the region and graft is often cited as a major problem by businesses operating in the country.