The apology comes after Mr Abe was criticised by Asian neighbours for previous comments casting doubt on whether the women were coerced.
Mr Abe told parliament: "I apologise here and now as prime minister."
This appears to be part of a concerted bid to reduce the fall-out of earlier comments, a BBC correspondent says.
Mr Abe said, during a debate in parliament's upper house, that he stood by an official 1993 statement in which Japan acknowledged the imperial army set up and ran brothels for its troops during the war.
"As I frequently say, I feel sympathy for the people who underwent hardships, and I apologise for the fact that they were placed in this situation at the time," he said.
His statement has gone a little further than similar attempts to clarify his position two weeks ago, but is unlikely to satisfy all his critics abroad, the BBC's Chris Hogg in Tokyo says.
The row over his comments have compounded the difficulties facing Mr Abe. His six-month premiership has already been rocked by a series of scandals and gaffes.
An opinion poll on Monday found public support for him - Japan's youngest ever prime minister - had shrunk to just 35%.
US resolution
Mr Abe provoked an angry reaction earlier this month after questioning whether there was any proof that the Japanese military kidnapped women to work as sex slaves during the war.
Mr Abe's comments drew sharp criticism from China and South Korea in particular, where many of the women came from.
Many historians believe Japan compelled up to 200,000 women - who also came from the Philippines, Indonesia and Taiwan - to become sex slaves during the war.
But some Japanese conservatives argue that the women were professional prostitutes who had been paid for their services, and any abuses were carried out by private contractors rather than the military.
Mr Abe's comments about the use of coercion were made as the US Congress began considering a non-binding resolution, which calls for Tokyo to make an unequivocal apology for the so-called comfort women.
Officials in Japan reject the idea that the prime minister should be told how to apologise by politicians from overseas, our correspondent says.
They say the draft resolution does not recognise the efforts that have been made to compensate the former comfort women.
Mr Abe's latest remarks in parliament have been made to clear up any misunderstanding and not as a result of outside pressure, they stress.
日本首相安倍晋三现已在国会就二战时期日本强征女性为慰安妇的做法做出道歉。
安倍告诉国会：“我现在以首相的身份就此（慰安妇问题）道歉。”
在安倍就此问题做出道歉之前，他曾因抛出“慰安妇是否为强迫暂无定论”这一言论而受到亚洲邻国谴责。
英国广播公司（BBC）的一名记者说，这似乎是降低安倍先前言论负面影响的努力中的一部分。
在日本议会上院的一场辩论中，安倍表示他赞同1993年的官方声明，在声明中，日本承认在二战期间其帝国主义军队曾为日本士兵设立慰安所，征用慰安妇。
他还表示：“正如我常所说的那样，我对那些遭受苦难的人们感到同情，我对她们当时被置于那种状况表示道歉。”
BBC驻东京记者克里斯·霍格（Chris Hogg）表示，这一声明比起安倍两周前为表明立场所做的类似努力似乎有进一步的发展，但仍不大可能满足国外的所有批评者。
安倍言论引发的广泛争议使他面临的局势更为复杂。他作为日本首相上任6个月以来已卷入一系列的丑闻和言语过失之中。
周一进行的一项民意调查显示，公众对这位日本史上最年轻的首相的支持率已跌至35%。
美国决议
本月早些时候，日本首相安倍晋三声称日军在二战期间强征妇女充当慰安妇这一说法缺乏证据，这一言论激怒了世界人民。
安倍的言论尤其遭到中国和韩国的强烈谴责，因为战时许多慰安妇都来自这两个国家。
许多历史学家都相信，日本在二战期间曾强迫多达20万的妇女充当慰安妇，这其中还有来自菲律宾、印度尼西亚和台湾地区的女性。
然而一些日本保守党成员狡辩说，这些妇女都是职业妓女，她们靠提供这种服务挣钱，而且任何虐待行为都是私人承包商实施的而非日本军队。
在美国国会开始考虑出台一项无约束力的决议，并督促东京政府对所谓的慰安妇进行明确的道歉时，安倍才抛出了“慰安妇是否为强迫暂无定论”这一言论。
本报记者称，日本官员对于首相应由海外政客告知该如何作出道歉这一说法表示反对。
他们声称，该决议草案并未认可日本政府先前对于慰安妇作出赔偿的努力。
他们还强调说，安倍最近在议会所做的言论意图澄清任何误解，而非迫于外界压力的影响。