Commissioner for Sports Gordon Oluoch said he would try and resolve their complaints, but did not commit himself to any specific action, and criticised the protesters for resorting to "the laws of the jungle".
A group of mostly low-level athletes swooped on the Athletics Kenya headquarters in Nairobi on Monday morning, ordering staff to leave and barricading themselves inside. Around about 60 were still there on Tuesday, said witnesses.
The Professional Athletes' Association of Kenya (PAAK) said it feared that honest athletes could face collective punishment because of scandals about doping and media allegations that top Athletics Kenya officials had embezzled some sponsorship money.
Athletics Kenya has denied all such allegations.
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Kenya, boasting some of the world's finest middle and long-distance runners, has in recent years been rocked by a spate of failed drug tests and the country's athletics federation has drawn criticism for not doing enough to tackle doping.
Allegations of corruption among Athletics Kenya chiefs tied to a Nike sponsorship deal, combined with Russia's recent ban from global athletics, have stirred fears that the East African nation could be banned from international track and field.
“We want to discuss the issues raised by the athletes to see if we can resolve the matter,” Oluoch said before a meeting at the Sport Ministry.
“We believe in the rule of the law. So even if the athletes have genuine cases, they must operate within the confines of the law, not through the law of the jungle,” said Oluoch.
Among athletes who joined talks at the ministry were Wilson Kipsang, president of PAAK and former marathon world record holder, and Wesley Korir, winner of the 2012 Boston City Marathon who is now also a lawmaker.
The international police body Interpol has said it will coordinate a global investigation into suspected corruption and doping in athletics, after an anti-doping commission report this month alleged widespread corruption and collusion in Russia.
Former International Association of Athletics Federations president Lamine Diack is being investigated by French police over allegations he received bribes to cover up positive doping tests of Russian athletes.
(Writing by Edmund Blair; Editing by Andrew Heavens)
