Sanchez, widely regarded as the finest player Mexico has produced, added that he wanted another chance to coach the national side but only when the current situation had been sorted out.
"I'm annoyed and disappointed with the way they are running the federation and the national team," he told Reuters in an interview after taking part in a meeting of FIFA's football committee.
"At the moment, they are confused and they don't know what to do," added the former Real Madrid striker.
"So, it's better to take advantage of this low point and replace them with people who have knowledge and capabilities.
"We need restructuring because there's no credibility, so we need to start again with a solid base."
Mexico's problems began in September when 13 players were disciplined by national teams' director Nestor de la Torre for holding a party at the team hotel after a friendly against Colombia in Monterrey.
Carlos Vela and Efrain Juarez were suspended for six months and the other 11, including Manchester United's Javier Hernandez, team captain Rafael Marquez and Giovani dos Santos, were each fined 50,000 pesos ($3,900).
Shortly afterwards, the 13 players asked not to be picked again until De la Torre was removed from his post.
Despite this, most of them were included in the squad for last week's friendly against Venezuela and warned they could face stiffer penalties if they ignored the call-up
They travelled for the match and De la Torre quit in an apparent victory for the rebels.
There was further confusion on Saturday when Victor Vucetich, one of two candidates to coach the national side along with Jose de la Torre, pulled out of the race.
"Like any Mexican, I'm delighted to help my country but in the future, this is not a good moment," said Sanchez. "That's why I understand Vucetich."
Sanchez coached Mexico for 16 months following the 2006 World Cup but was fired after the under-23 team failed to qualify for the Olympic Games, something which still rankles.
"My job was the senior team but they put me in charge of the under-23 and Panamerican Games teams as well," he said.
"You can't make a coach responsible for three national teams.
"The senior team was doing well, we finished third at the Copa America in 2007, we beat Uruguay and Brazil and I was fired because of something else which shouldn't have been my responsibility."
Sanchez had kinder words for Jose Mourinho, the latest coach at his former club Real Madrid.
"He'd doing well," said Sanchez. "There has to be discipline and it's producing results because Real Madrid have always had difficulties in defence.
"Now they have discipline in defence and the results are proving them right."
