The disclosure is likely to add to criticism of the Obama administration's military strategy, with US Senator John McCain saying that the United States was "losing" the fight against the extremists, who have overrun large areas of Syria and Iraq.
Several lawmakers including McCain, the 2008 Republican presidential nominee, grilled Carter and the military's top general, Martin Dempsey, on topics ranging from Ukraine to the Middle East.
Carter said the US was training about 60 fighters as of last week.
"This number is much smaller than we had hoped for at this point," he added, pointing to difficulties in vetting suitable candidates.
"We know this program is essential. We need a partner on the ground in Syria to assure ISIL's (IS) lasting defeat."
McCain criticized what he called "not a very impressive number."
McCain said the "reality" on the ground is that IS jihadists continue to gain territory in Iraq and Syria, while expanding their footprint across the Middle East, Africa and Central Asia.
"There is no compelling reason to believe that anything we are currently doing will be sufficient to achieve the president's long-stated goal of degrading and ultimately destroying ISIL -- either in the short-term or the long-term," McCain said at the Senate Armed Services Committee, which he chairs.
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