Capita, which is administering the congestion charge, said the six-hour outage occurred during a failover test conducted by telecoms firm Cable & Wireless, which provides the connectivity behind the website.
"Cable & Wireless rectified the problem and we are back to normal," a spokesman said. Cable & Wireless said it was taking "additional measures" to avoid a repeat of the problem.
The spokesman added: "These measures include further checks on the website to ensure that any future procedures are even more robust."
James Roper, chief executive officer of industry body the Interactive Media in Retail Group, said: "They have to get this right - the problems with traffic in London are so acute that it's not acceptable if this major initiative is launched as an unfinished solution.
"They should make sure that it is working consistently and reliably before it is put in front of the public," he added.
Last year, Transport for London awarded Capita a five-year contract worth around £230m to administer the congestion-charging scheme, with a possible two-year extension.
A spokesman for Transport for London said: "Clearly we are very disappointed that it was down but we are pleased that steps have been taken to rectify it so quickly."