Sara Khan said some stories have left her “heartbroken”, while the problem is increasing in scale and becoming more professionalised.
The Commission for Countering Extremism (CCE), which Ms Khan heads, was set up last year following the Manchester Arena bombing.
On Wednesday, it launched an evidence gathering programme with the aim of producing an in-depth report on how to confront all forms of extremism.
In an interview with Sky News, the commissioner admitted she herself has received death threats, but remains undeterred from carrying on with her work.
Ms Khan has campaigned for women’s rights in Muslim communities for many years.
After her appointment in January, she faced immediate calls to quit from some Muslim groups and politicians because of her support for the Home Office’s Prevent counter-terrorism strategy.
It led to claims Ms Khan was too close to the government and wouldn’t be able to gain trust in some communities.
“When I started working in the space about 10 years ago, if someone had said to me the amount of abuse, fake news, smears, vilification, death threats I would get, I don’t think I would have believed you,” she said.
“But, it’s given me a very thick skin and it’s made me realise I’m going to press on.
“I’m not going to go away because this issue of extremism matters too much to me – and it is too big an issue facing our country.”
Since January, Ms Khan has visited 10 towns and cities and spoken to 300 experts and faith leaders.
In Newcastle, marches by far-right extremists were damaging business in the city, while youth workers “are concerned about the sheer scale of far-right extremist propaganda online, and the lack of counter messages,” she said.
Ms Khan added: “I went to Leicester where activists said extremist preachers were promoting sectarianism and hatred behind closed doors, so it becomes impossible to challenge.
“But many of these people would then come out and give messages of peace.”
Ms Khan talked of a “changing face” of extremism which is becoming “more intellectualised and more professionalised”.
The commissioner believes there is not enough support for people who challenge extremism.
She said: “I have been both inspired and heartbroken by stories of ordinary people in our towns and cities who on a voluntary capacity are challenging extremists because they can see how they are trying to divide our communities and groom young people.
“Stories of the abuse, vilification, threats, smears to their reputation – and these are brave unsung heroes in our country. They want support.”
In the coming months, the CCE will examine academic evidence on extremism, bespoke research and issue a public call for evidence.
It will ask victims, regulators, local councils and police forces, universities and other public and private bodies to share information.
The evidence drive will be used to present solutions for tackling the issue.