It follows intense public pressure after a parliamentary inquiry into the devolution ministry, where officials are alleged to have massively inflated government purchases, including claiming to have bought simple pens for USD 85 (79 euros) each.
Devolution and Planning Cabinet Secretary Ann Waiguru, who denies any wrongdoing, said she was stepping down for health reasons but admitted there had been problems in her ministry.
"I will be the first to admit mistakes were made, some officers... Abused the discretion granted to them and the trust placed on them," Waiguru said, who took the post in May 2013.
In a rare joint show of force, a dozen ambassadors from key donor nations -- including the United States, Britain, France, Germany and Japan -- warned that corruption was "undermining Kenya's future."
President Uhuru Kenyatta yesterday however said it had been "an important week for the fight against graft" in Kenya.
"This week alone 72 individuals including a principal secretary and five managing directors were arraigned in court on corruption related offences," Kenyatta's office said in a statement.
Kenya, which is placed near the bottom of Transparency International's annual corruption index, coming in 145th out of 174, has long been blighted by graft.
