"We are late, we face difficulties and risks right up to the last minute because we haven't tested the installations, we need time to test them," Valcke told reporters in Rio after meeting with members of the Brazilian government and Local Organising Committee.
"It's a lesson and definitely we will act differently and we will have to find a different way of working in Russia in 2018," Valcke said.
Brazil will host the World Cup in June and July but it faces a mad rush to get everything ready in time.
Three of the 12 stadiums are still not complete, including the Arena Corinthians in Sao Paulo that is due to host the opening match between Brazil and Croatia on June 12.
That arena and some others have yet to install the telecoms networks that will be used for broadcasters and media.
Originally, organisers said those networks had to be in place 90 days before the competition began in order to properly test them but with 77 days to go before the first ball is kicked work has not yet started.
"This is the last big challenge for the World Cup," Deputy Sports Minister Luis Fernandes told Reuters.
"After that the challenges are operational, in other words, holding the test events to see if we can make things better."
FIFA now says important test events will take place in Cuiaba on April 26, in Curitiba in mid May, and on May 17 in Sao Paulo. Those three stadiums were supposed to be ready in December but they are still not complete. Twelve stadiums will be used in all.
One other issue is the lack of progress on the temporary installations such as hospitality tents and storage containers that will be brought in to help with the energy, security and sponsors areas outside the stadiums.
Valcke said last week Sao Paulo had resolved the issue but on Thursday back-tracked and said he expected a resolution this Friday.
Porto Alegre city council voted on Tuesday to award tax breaks to companies who invest in the installations, paving the way for work to begin. Valcke said he hoped the first containers would be in place outside the Beira Rio stadium by April 15.
Valcke, who caused a diplomatic incident two years ago when he said Brazil needed a "kick up the backside" to speed up their work, complained of the reaction when he criticised the home nation's preparations.
"Every time I said something a bit hard you the media said I am the worst person in world," he said.
Valcke said FIFA would learn from its mistakes and do things differently in Russia and particularly Qatar, which will have fewer stadiums.
- Sports & Recreation