"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.
But his pronouncements did little to appease groups such as Human Rights Watch, who have said the World Cup could leave an important legacy of improved working conditions and labour laws in Qatar.
"The weak message Blatter sent today is the same one FIFA sent in 2012 when Human Rights Watch presented them with allegations of forced labour in Qatar — the basic rights of workers building Qatar's 2022 World Cup is somebody else's problem," the group said in a statement.
"Blatter's assertion that there is 'plenty of time' to resolve the issues in Qatar would suggest he is either ignorant of or indifferent to the
appalling abuses happening right now in Qatar."
Gulf countries have faced regular criticism in the past over their rules on migrant workers 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.
The International Trade Union Confederation, which raised the alarm in August and is sending a delegation to Qatar next week, warned that at current rates, 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.
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.
the head of Qatar's World Cup committee, Hassan Al Thawadi, 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, 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 have protested, fearing disruption 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 argued that June and July were 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 .
But FIFA opted to keep discussions boiling, promising a consultation with interested parties, as well as players, clubs and "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."