A strongly-worded statement from Qatar's Government Communication Office, claimed "enormous damage has been done to Qatar's image and reputation" by the article, "The Human Toll of FIFA's Corruption".
Doha said in the statement that no one has died on World Cup construction sites.
"An article in the Washington Post... Claimed that 4,000 workers are likely to die while working on World Cup sites and that some 1,200 had already lost their lives," read the statement.
The statement added that article meant "readers around the world have now been led to believe that thousands of migrant workers in Qatar have perished, or will perish, building the facilities for World Cup 2022 -- a claim that has absolutely no basis in fact".
More From This Section
The article, which was posted online on May 27, has been viewed more than five million times, said Qatar.
Doha says it wants the article corrected and retracted.
Qatar said it had written to the Washington Post to complain but was told because the "article had appeared online and not in print", the letter would not be published.
Doha said the calculation made no distinction for how those deaths occurred.
It said 400 people would die from cardiovascular disease each year and these deaths would have occurred "even had they remained in their home countries".
On its website, the Post said the story had been "updated to reflect the fact that figures include total migrant worker deaths in Qatar, not just World Cup-related deaths".