The energy-rich Gulf emirate has been under mounting pressure to improve the working and living conditions of migrant labour building the multi-billion-dollar infrastructure for the tournament.
The International Trade Union Confederation report is "littered with factual errors and attempts to discredit the positive work we are undertaking," Qatar's World Cup organising committee said.
The ITUC said its general secretary, Sharan Burrow, found during a site visit to Al-Wakrah Stadium "38 World Cup workers from India, Nepal and Thailand living in squalor with mattresses on the floor in makeshift rooms underneath the bleachers or stadium seats."
The Qatar committee said the ITUC report referred to accommodation not being used by construction workers on the stadium.
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"Our 108 construction workers live in a refurbished accommodation on Street No 23 in Doha's Industrial Area, which has been visited by TV crews," the committee said.
It said the ITUC "never visited our accommodation, nor requested to do so."
"No one has died on World Cup projects," it said, although the report did not mention deaths among construction workers.
The embassy did not give details about the circumstances of the deaths, but the ITUC said the data showed an "exceptionally high mortality rate."
An official at the Nepalese embassy told AFP in January that 191 deaths had been registered in 2013, many of them from "unnatural" heart failure, and 169 the year before.
Most of the labourers working on the new stadiums and vast infrastructure projects ahead of football's biggest tournament in Qatar are from South Asia.
Qatar in February published a set of guidelines aimed at protecting the rights of thousands of expatriate workers employed on its construction projects.