Last year, a quarter of charities broke the law by failing to send in accounts within the 10-month deadline, the commission says. This has left £6bn of charity money unaccounted for.
"Charities do tremendous work, but many need to become better at accounting to the public for what they do," said Andrew Hind, chief executive of the commission.
The commission has named 11 out of Britain's 100 biggest charities that filed their accounts late. These include Save the Children, Elim Foursquare Gospel Alliance and the Royal Opera House.
But Leonard Cheshire, another of the offenders, felt public shaming was unfair. "We have consistently filed all documents on time with the commission," said David Kay, director of finance at the charity. "This year we filed the annual return on time, on 24 January.
"On 3 April, we received a call reminding us to file the accounts. We immediately sent a second copy, the receipt of which was acknowledged on 4 April."
Nacro blamed a change in finance directors for its own late submission.
"Being marginally late in submitting our accounts does not mean we are not financially accountable," said Paul Cavadino, its chief executive.
The commission defended its decision, however. "It's essential that the public realises where the money is going and that it is properly accounted for," a spokeswoman said.
Sir Digby Jones, outgoing director general of the CBI, said: "There's no reason why the top 100 charities can't adopt the same standards as the private sector when it comes to filing accounts."