The force has employed more officers in the area, but policing the internet remains a "massive challenge", Sir Bernard Hogan-Howe said.
Sir Bernard said there is a "real logistical problem" juggling online crime with other police roles.
Funding cuts have hit their ability to tackle the range of crimes, he added.
Earlier this week, Her Majesty's Inspectorate of Constabulary said police forces in England and Wales need to address failings in child protection.
HMIC said it found poor practice in more than a third of cases it looked at and anticipated this would apply to all police forces.
Sir Bernard said the Met had a squad of 300 officers dedicated to internet security which is likely to grow by 200 in the next year.
But he added: "Even then I think we're skimming the surface a bit."
"We're trying to do all these other things as well: the pubs all turn out tonight and there will be fights, there will be big armed robberies, there will be anti-social behaviour, there will be 70,000 marchers in London - everybody expects all of this doing... there's a risk assessment process that says in these cases what's the risk of that person hurting a young person today," he said.
Sir Bernard was questioned by a panel for Sky News' Hotseat programme.
"One of the problems we do have is that you get less and less money spent on policing at the moment. Probably a third less over the next two years, so there's going to have to be some hard decisions made by society and by the police," he said.
"It's incredibly important but there are also other things too which we have to see to so we do our best to put as many resources as possible to work our way through it but there's no doubt it's a massive challenge."
Sir Bernard also said police arrest an average of one person per day for terror-related offences, up a third from last year, adding that "we've disrupted some significant plots".
Police are only "skimming the surface" despite efforts to protect children online, the Metropolitan Police's commissioner has said.