In a tweet (in French), the Minusma mission also called for calmÂ in the impoverished West African nation.
This comes after reports that interim President Ndaw and Mr Ouane were driven by soldiers to the Kati military camp near the capital, Bamako.
This raised fears of a second coup within a year in the country.
Defence Minister Souleymane DoucourÃ© has also reportedly been detained.
Late on Monday, Mr Ouane told AFP in a phone call that soldiers "came to get him". The news agency said the line was then cut.
The African Union, the Economic Community of West African States, the EU and the US also condemned the arrests, saying Mali's top politicians must be released without any preconditions.
The reported detentions came just hours after a government reshuffle, which saw two senior army officers who took part in last year's coup replaced.
Once again Mali is looking unstable just nine months after the military coup that saw President Ibrahim Boubakar KeÃ¯ta removed from office, the BBC's Africa editor Will Ross reports.
He says that many Malians had welcomed Mr Keita's departure - but there's anger at the dominance of the military in the transitional government and the slow pace of promised reforms.
A previous coup in 2012 led to militant Islamists exploiting the instability to seize territory in northern Mali.
French troops helped regain territory, but attacks continue.