Colaco was handed the ban by the FIFA Ethics Committee for "accepting a payment in the context of the elections" for former Asian Football Confederation chief Mohamed bin Hammam's FIFA executive committee seat in 2009.
Bin Hammam, now out of football-related activities after a life ban imposed by FIFA, beat current AFC chief Sheikh Salman Bin Ebrahim Al Khalifa of Bahrain 23-21 in the 2009 elections marred by allegations of vote-buying from both candidates' supporters.
"The adjudicatory chamber of the FIFA Ethics Committee, chaired by Hans-Joachim Eckert, has decided to ban the former General Secretary of AIFF Alberto Colaco, from taking part in any kind of football-related activity at national and international level for a period of three years," the FIFA said in a statement on its official website.
"Colaco accepted a payment in the context of elections for the FIFA Executive Committee at the AFC Congress in May 2009 - won narrowly by Mohamed bin Hammam - while he was serving as the General Secretary and voting delegate of the All India Football Federation.
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FIFA said that the ban on Colaco would be effective from today.
A top football administrator told PTI that Colaco's ban by the FIFA has brought shame on the country's football fraternity.
"As far as I remembered, this is the first time an Indian official has been banned by FIFA and that too for taking bribes. It has surely brought shame on Indian football," he said.