A Belgian environment minister has been forced to resign after falsely claiming the country’s intelligence services held evidence that children skipping school to demonstrate over climate change were being directed by unnamed powers.

Joke Schauvliege, a minister in Flanders, where the school-strikes movement first emerged, provoked a wave of criticism of the wider political class after suggesting the protests were a “set-up” and “more than spontaneous actions of solidarity”.

“I know who is behind this movement, both of the Sunday demonstrations and the truants,” Schauvliege had told an audience of farmers. “I have also been told that from state security. I can guarantee that I do not see ghosts alone and that climate demonstrations are more than spontaneous actions of solidarity with our climate.”

The comments prompted a rare denial by the Belgian state security services. “We have not reported anything about this to Schauvliege,” they said. “Neither verbally nor in writing.”

The minister initially sought to hold on to her position insisting that she had not lied, but merely gone “too far”. “In recent weeks, I have slept little and I was overwhelmed by frustration, I am a human being and I could be wrong,” she told the Flemish channel Radio 1.

But during an emotional press conference on Tuesday afternoon, Schauvliege announced that she could not continue in her post given the growing controversy. “It is difficult to continue to function as climate minister in these circumstances,” she said, between tears.

Tens of thousands of Belgian children, inspired by the lone protest launched last year by Greta Thunberg, then 15, outside the Swedish parliament, have played truant from school in recent weeks to march on the streets of Brussels, Liège, Namur and Leuven. School strikes have been also been held in Germany, Switzerland and Australia and a global School Strikes 4 Climate Action march is set for 15 March.

Belgium has four environment ministers – one for each region and at the national level – but it has no national policy to reach the 2030 goal set by the UN of limiting global temperature rise to well below 2C, and strive for 1.5C.

Anuna De Wever, the 18-year-old Flemish student who first sparked the demonstrations in Belgium, had described the claims by Schauvliege, a member of the Flemish Christian Democrats, as “manifestly not true” and an “insult to the youth”.

“It is very strange that a minister can lie about such a thing,” she said. “That’s just not the case. Can we stop doubting the movement?”

The largest march so far in Belgium, two weeks ago in Brussels, saw 35,000 children demonstrate.

A spokesman for Youth for Climate, the organisation set up by De Wever to organise the protests by schoolchildren, said the comments were in keeping with the Belgian authorities’ failure to commit to international climate change goals.

“The minister’s allegation is an insult to the authentic engagement of so many young people,” they said in a statement before the announcement of Schauvliege’s resignation.

The Flemish minister-president, Geert Bourgeois, had described the environment minister’s comments as “unfortunate”.

The response of Flemish politicians to the climate change demonstrations has come under heavy criticism.

The chairman of the Flemish nationalist party the New Flemish Alliance, which was until recently in government, last month urged the young protesters “not to believe in the apocalypse” but to go back to their books and have “confidence in the future and in the power of innovation”.