The DUP has accused the Ulster Unionists and the SDLP of trying to bring down the assembly.
A marathon assembly debate was held at Stormont
Both parties voted against their executive colleagues, Sinn Fein and the DUP, after a marathon debate at the assembly on Monday night.
They backed an Alliance party amendment which said the draft programme for government and the draft investment strategy showed "limited vision".
The Alliance motion was defeated by 24 votes to 50.
But Alliance leader David Ford said the executive was "yet again in crisis".
"This is the second time in a week that the Ulster Unionists and the SDLP have voted against their executive colleagues," he said.
"The PfG is a massive missed opportunity and the public are now seeing how directionless the executive is."
The DUP said the structure of the assembly was built around a mandatory coalition, principally negotiated by the Ulster Unionist Party and the SDLP.
Finance Minister Peter Robinson said: "The basis upon which any coalition government can move forward is on the basis for a programme for government.
"And so that there is no doubt at a later stage, without an agreed programme for government, there cannot be government."