Two high-ranking officers have been suspended from Rwanda's military and put under arrest, a military spokesperson told the BBC.
Maj-Gen Charles Muhire has been accused of corruption and misuse of office, Lt-Gen Karenzi Karake of immoral conduct.
This comes just days after a reshuffle in Rwanda's military leadership and ahead of elections due in August.
It follows reports in a local newspaper that the men had misunderstandings with President Paul Kagame.
However, the government has dismissed these reports as rumours.
A few days later, the Kinyarwandan (one of Rwanda's official languages) independent newspaper was suspended for publishing false information and inciting resentment in the army, says the BBC's Geoffrey Mutagoma in Kigali.
Investigations into the two generals' alleged crimes are still underway and it is still not clear whether their cases will end in trials, Rwandan army spokesperson Maj Jill Rutaremara told the BBC.
Our correspondent says the two generals are popular and important figures in the Rwandan military.
Gen Karake is a former director of intelligence and deputy head of the African Union-United Nations peacekeeping force in Darfur, Sudan.
Gen Muhire is a former air force chief.
Both men held top positions in the military campaign conducted by the Rwandan Patriotic Front (RPF) to end the 1994 genocide.
BBC Great Lakes analyst Kasim Kayira says the arrests will be seen by ordinary Rwandans as further evidence of divisions in the military.
A few months ago, President Kagame increased the salaries of his Presidential Brigade - the soldiers responsible for guarding the president - but not those of other military personnel.
Rwanda's next presidential polls are due in August 2010 and Mr Kagame is expected to seek re-election.
Our correspondent says the president still exercises effective control over the military and the army are unlikely to destabilise the forthcoming elections.