The Assembly has approved the Executive's Programme for Government.
The programme, the first to be formulated by a devolved Northern government, sets goals for the lifetime of the current Assembly and beyond.
Although members of the DUP work as Ministers in the Executive, the party, and the pro-agreement Alliance Party, voted against the programme.
Proposing the motion to accept the programme, the First Minister said the anti-agreement DUP had participated fully in preparing it.
"The DUP may have their own particular way of communicating with the administration, but they do participate and their contribution is contained within this collective programme," Mr Trimble said.
The Regional Development Minister, Mr Gregory Campbell of the DUP, said participation in the system did not equate to supporting it.
"Participation in any system, however indirect and however faulty it might be, will not negate the DUP's position in terms of running away from our mandate," Mr Campbell said.
Mr Ian Paisley jnr of the DUP called on members not to allow "evil to prosper" by voting for the programme.
Supporting his party's amendment to reject the programme, Mr Seamus Close of the Alliance Party said it was not sufficiently radical to tackle divisions and tribalism.
"The Executive to many degrees is still putting party before country. They are fighting the battles of yesterday rather than acting as a cohesive group to eradicate the problems of Northern Ireland," he said.
Prof Monica McWilliams of the Women's Coalition agreed that the Ministers making speeches had failed to set an example in their relations with each other.
"It is disappointing to see the extent to which they have not been pulling together in a cohesive and inclusive fashion," she said.
Mr Edwin Poots, of the DUP, noted it contained a number of targets for women's health but none for treating male cancers.
Mr Barry McElduff, of Sinn Fein, was also critical in part but spoke of facing the electorate "with the Programme for Government in one hand and the Good Friday agreement in the other".
Mr Patrick Roche of the Northern Ireland Unionist Party said the Programme focused on redistribution at the expense of wealth creation.
The Assembly accepted the motion endorsing the programme by 47 votes to 27.