The National Front's headquarters were raided by police Monday when Le Pen was on a trip overseas as part of the same investigation.
But Le Pen told reporters that she hadn't been required to wear a headscarf when she met Egypt's top cleric in 2015.
After meeting Hariri on Monday, Le Pen went against current French policy in Syria by describing President Bashar al-Assad as the "only viable solution" for preventing Islamic State from taking power in Syria.
"This is the protocol", the statement said. Le Pen has proposed extending the 2004 law banning headscarves and other religious symbols in all public spaces.
Le Pen's chances of winning the second round have vastly improved over the past week as her main rivals Francois Fillon and Emmanual Macron are marred by scandal.
She met president Michel Aoun and prime minister Saad Hariri but refused to meet the grand mufti because she was asked to wear a veil. She emphasized the need to provide more aid to Lebanon that had sheltered over 1,500,000 Syrians, in order to prevent them from moving to Europe.
Le Pen reportedly refused to put it on and the meeting was cancelled.
"The mufti's office regrets this inappropriate behaviour in such meetings", the statement said.
There was also apparent displeasure at her comments on Assad, including from some Lebanese allies.
Le Pen isn't the only candidate with legal issues.
Christian right-wing leader Samir Geagea said after meeting with Le Pen that "terrorism has no religion". While the terrorist militia Hezbollah - which is represented in the cabinet - is an active supporter on the ground of the Assad regime, many Sunnis sympathize with the anti-Assad opposition.
According to Politico, Ms Le Pen is leading the latest polls with 27 per cent of the vote - with former economy minister Emmanuel Macron and ex-prime minister François Fillon, the conservative frontrunner, unchanged at 20 per cent each.
The first round of the presidential elections will take place on April 23 and a second-round runoff on May 7.
Le Pen is the favourite to make the final round of the election in May, but so far Macron and Fillon have been inseperable in the polls.