"I express all my sympathy and regret for anything that happens in any country where there are deaths on construction sites, especially when they are related to a World Cup," Blatter told reporters as FIFA wrapped up a crunch two-day meeting behind closed doors at its Zurich base.
Earlier, on his Twitter account @SeppBlatter, he said: "FIFA cannot interfere with the labour rights of any country, but we cannot ignore them".
To date, Blatter had avoided public comment on the storm raging since a report by Britain's The Guardian newspaper last week that migrant labourers faced "modern-day slavery" on Qatar's World Cup sites and were paying with their lives.
Gulf countries have faced regular criticism in the past over their rules on migrant workers and the treatment they face, but the World Cup link has added new impetus to the debate.
The Guardian's findings were based on documents from Nepal's embassy in Qatar, an oil- and gas-rich emirate where at 370,000, Nepalese labourers are the second largest group after Indians.
According to the International Trade Union Confederation, which raised the alarm in August and is sending a delegation to Qatar next week, if current death-rates continue, at least 4,000 workers could perish before the 2022 World Cup even begins.
Beyond the fatalities, critics also slam the confiscation of passports, withholding wages for long periods, debts to recruiters, insufficient drinking water in high temperatures, and squalid camps for labourers.
Amnesty International, which says such practices are tantamount to forced labour, is set to publish an in-depth report on Qatar next month.
Qatar repeatedly rejected claims over slavery-style conditions on construction sites in the emirate, the world's wealthiest nation per capita.
It says it takes its international commitments seriously, and has announced plans to double its number of labour inspectors to 150 -- though critics question the impact.
Arriving on Thursday at FIFA, Hassan Al Thawadi, head of Qatar's World Cup committee, said worker deaths were a stark issue and insisted the government was dealing with it.
"Is this acceptable? Of course it isn't. The government has said so quite clearly," he told reporters.
"We are going to ensure the security, the protection and the honour of everyone. We've worked to that pledge, will continue to do so, and will always give it the utmost priority," he added.
FIFA's 2010 decision to name Qatar to host the 2022 edition of the international game's showcase tournament was dogged by controversy from the outset.
Even before the renewed claims over the treatment of migrant labourers, Thursday and Friday's session of FIFA's executive committee had been expected to focus heavily on Qatar due to a bitter debate over the 2022 timing.
The world of football is split over whether to shift the World Cup from its traditional June and July slot to the winter in order escape the scorching Gulf heat - a climate issue that critics say could hardly have escaped FIFA's notice.
European leagues are up in arms, saying the move would cause havoc to their fixtures and coffers, while winter sports federations and broadcasters argue that a high-profile football event clashing with their own seasons would dent television audiences and revenues.
Blatter has argued that June and July are never set in stone, and that rescheduling would reflect football's global appeal by showing that anyone can host the World Cup.
"The tournament will be contested by 32 teams. This is not a binding statement that the tournament should take place in June or July," he said Friday.
But FIFA opted to keep discussions boiling.
"Because there has been a great deal of noise we have decided now there should be a consultation where we will bring together all the organisations dealing with the organisation of the World Cup," Blatter said, citing leagues, players and clubs, as well as "economic stakeholders".
Some critics have said Qatar should simply be axed as host, but Blatter shot that down, saying: "The Fifa World Cup 2022 will be played in Qatar. There you have it."