Mak Chishty described Saturday's terror attack in London, which was claimed by the so-called Islamic State group, as "an attack on all communities".
Seven died in the attack, with 48 hurt. The attackers were shot dead by police.
"Terrorism and extremism is hurting Islam," said Mr Chishty - the highest-ranking Met officer of Muslim faith.
"Every time a terrorist attack takes place, Muslim communities either face, or fear, a backlash against them," said a statement read by Mr Chishty on behalf of Muslim community groups.
"The Muslim community appeals to all sections within their own communities to root out the scourge of terrorism which hides amongst their own people and masquerades as Islam.
"The Muslim community is alarmed and concerned that this attack by three people, which would have required planning, was not reported."
The three attackers drove a van into pedestrians on London Bridge and launched a knife attack in Borough Market before being shot by police.
It was the third terror attack in the UK in three months, following the car and knife attack in Westminster in March, in which five people were killed, and the Manchester bombing on 22 May, when 22 people were killed.
Speaking outside New Scotland Yard, flanked by Muslim community leaders, Mr Chishty added: "It is the Islamic duty of every Muslim to be loyal to the country in which they live and we are now asking questions to understand how extremism and hatred has taken hold within some elements of our own communities.
"Muslims must do more to stop such attacks from happening again and we want to know how we can play a greater role in the future."
The Muslim community must "root out the scourge of terrorism which... masquerades as Islam" a Met Police commander has said.