Tens of thousands of schoolchildren have protested across Belgium for the past four Thursdays.
In tears, Joke Schauvliege admitted there was no plot against her but denied lying.
She said she had been personally targeted by thousands of text messages.
"I couldn't communicate normally any more, I couldn't communicate with my family and I let myself get carried away by it," she told a press conference.
Pressure had been building on the Flanders regional minister to resign after she told a farmers' union audience at the weekend that state security had informed her that recent climate protests by children skipping school and others were "a set-up".
She pointed to unnamed environment groups that she accused of seeking revenge against her for years for backing agriculture groups.
State security denied her claim, prompting the minister to apologise.
"I admit I've never had direct contact with state security," she said on Belgian radio. "I didn't lie, I went a bit too far."
Climate activists were stunned by her remarks. Anuna De Wever, an 18-year-old student who has helped organise the Thursday school strikes in Brussels and other cities, said the minister's "lies" were an insult to young people.
Further protests in Belgium are set to take place this week. The school actions have been co-ordinated by children themselves and there is no suggestion that they are anything other than spontaneous.
Dutch schoolchildren are planning a separate demonstration in The Hague, and there have been separate protests in Germany and Switzerland.
However, the campaign of text messages and emails, which Ms Schauvliege said were sent to her day and night, has shone a light on the tactics of pressure group Act for Climate Justice.
The organisation has made public the mobile phone numbers of all four Belgian environment ministers, urging Belgians to contact them.
Posters appeared on billboards directing people to a website with the messages "Stop climate criminals" and "call your ministers".
A linked page gives four separate buttons to send the ministers an email, text or tweet or make a phone-call. The website itself claims 41,000 people who have already done so. Some 6,000 have sent a text message.
Although the campaign is apparently over, a spokesman for the group, Arno Kampynck, told Flemish TV that the mobile numbers were work numbers rather than private, and all the ministers had to do was have a separate phone for personal calls.
This is unlikely to be the end of Joke Schauvliege's political career. She is still considered widely popular in East Flanders and is expected to run at the head of her CD&V party's list in elections in May.
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