Royal told RFI ahead of the meeting that it would be the occasion for her to "answer for" her record during two years in office, "in particular over energy transition and the vote on the biodiversity law".
Hundreds of politicians, activists, employers and trade unionists were set to take part in roundtable discussions on key environmental concerns, with Hollande speaking on Monday and Prime Minister Manuel Valls closing the meeting on Tuesday.
But many NGOs accuse the government of failing to deliver on the 396 decisions adopted by the four preceding conferences.
"Ever since the first one we felt that it was pointless and the we'd get nothing from these enviromental conferences, that we were there to give the impression that the government really wanted to do something about the ecology," Jean-François Julliard, the head of Greenpeace France, told RFI to explain why his organisation would not be attending.
And the CGT union last week announced that it would not go to a conference that was "completely out of touch with the realities of working life and ... workers' aspirations and demands".
Some Green Party MPs are also boycotting the meeting.
Among the points of contention are:
The biodiversity bill has not yet been passed by parliament;
The energy transition law was passed last summer but the majority of decrees putting its provisions into effect have not yet been signed;
Nuclear power provides 75 percent of France's electricity, despite Hollande's campaign promise to reduce it to 50 percent by 2025;
The Notre Dame des Landes airport, which has been opposed by an occupation of the site by militant ecologists and farmers, has not been scrapped despite a critical experts' report but the project will be put to a local referendum on 26 June;
Rail transport was to be favoured as environmentally friendly, the last conference decided, but a recent law opened up competition to road passenger coaches and petrol prices are falling, leading to calls for a carbon tax of 40 euros per tonne to reverse the effect.
After signing the Cop21 climate agreement at the UN on Friday, Hollande told the conference that French would be the first country in the world to issue "green bonds" and pledged to reduce the country's reliance on nuclear power.
Power company EDF would announce the closure of some nuclear power stations in 2018 after the publication of a review by the Nuclear Safety Authority, he said.
The Fessenheim reactor in eastern France would be the first to close, Hollande added, and a decision as to when will be taken this year.
Royal has promised to issue a decree fixing renewable energy targets on Wednesday and a roadmap for nuclear power before 1 July.
She plans to raise renewable energy capacity by 50 percent by 2023, largely by raising the output of land-based wind turbines from 23,000MW to 26,000MW and solar energy to 20,000MW, measures that would create 40,000 jobs, according to the minister.
To read our coverage of the Cop21 climate talks in Paris, click here