Military forces this month surrounded the home of Prime Minister Carlos Gomes in a coup just weeks before a runoff election. Gomes secured 49 percent of the vote during March presidential elections, which wasn't enough for a clear victory.
Gomes and acting President Raimundo Pereira are in custody.
The Security Council called for the release of both leaders and warned authorities in Guinea-Bissau they could become the target of international sanctions.
"The Security Council demands the immediate restoration of the constitutional order as well as the reinstatement of the legitimate government of Guinea-Bissau," a statement read.
The African Union and Economic Community of West African States last week rejected plans by the military to launch a two-year transition plan. The AU suspended Guinea-Bissau following the coup.
The Council of the European Union expressed disappointment with the coup in the West African country.
"Self-appointed transitional institutions will not be recognized, nor any kind of arrangement which would allow the armed forces to continue to threaten or control the civil powers," the council said in a statement Monday.