The questioning outside parliament's ordinary session, a rare occurrence, underscores the ruling Liberal Democrat party's eagerness to regain public trust.
Abe is expected to reshuffle his Cabinet next week, after seeing public approval sink following various scandals and his party's railroading of unpopular legislation.
Today's questioning was over allegations that Abe intervened to help a friend, Kotaro Kake, gain approval to open a veterinary school in western Japan.
"I only instructed to speed up efforts for the deregulation reforms. I have never issued instructions on specific cases," Abe said. "The approval is a result of the process that was appropriate and open."
The school scandal erupted after a whistleblower and former top education ministry bureaucrat, Kihei Maekawa, came forward to say that Abe's office had had significant influence over the school's approval and distorted the decision.
He and other witnesses, including bureaucrats and two former members of the Abe-commissioned panel on the school, said they were not directly instructed by Abe.
Given the lack of significant center-left alternatives or strong rivals within his party, Abe's tenure as prime minister is not under immediate threat.
Still, Abe, in his second stint as prime minister, is getting the message that he might have to tread a bit more softly in pushing for some of his top political priorities, such as revising Japan's war-renouncing constitution.
Results from Mainichi newspaper polls taken over the weekend show that support ratings for Abe's Cabinet stood at 26 per cent, down 10 points from last month, with 56 per cent disapproving of his government.
Sixty-two per cent of the respondents said Abe should step down when his term ends next year, while only 23 per cent supported his extended leadership.
Abe is also under fire for not replacing his protege, Defense Minister Tomomi Inada, despite repeated scandals. The latest one involves an alleged cover-up of internal documents, including the daily activities and safety conditions of Japan's Self-Defense Force during its UN peacekeeping operations in South Sudan.
Yesterday, their candidate lost a closely watched mayoral election in Sendai, in northern Japan.
The losses in the polls are a major setback for Abe because much of his party support was for his record of election victories. Abe, who took office in late 2012, was seeking a third term when his term ends in 2018.
During the questioning today, Abe acknowledged that Kake, director of a major education organisation, was a friend even before he became a lawmaker in 1993.
But he said Kake has not tried to tap Abe's position or influence to obtain preferential treatment and did not discuss with him his plans to open a new veterinary school in Imabari, in western Japan.
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