The Kremlin published introductory remarks by Putin and Grossi at the meeting in Sochi in southern Russia but gave no details of the closed-door meeting that followed.
Putin told Grossi he was prepared to discuss "particularly sensitive and important issues on the agenda ... and do everything to ensure security anywhere we are in one or another involved in nuclear energy", the Kremlin said.
Grossi met the head of state nuclear power company Rosatom Alexei Likhachev alongside Putin.
Russian forces seized Europe's largest nuclear power plant in their 2022 invasion of Ukraine and have occupied it since. Grossi is due to meet Putin in the southern Russian city of Sochi later on Wednesday.
Zaporizhzhia lies close to the front lines in a part of southern Ukraine which Moscow claims to have annexed. All six of its reactors are shut down, but it requires constant power and a water supply to keep it cool and prevent a potentially catastrophic meltdown.
It was damaged by fire when it was taken over in March 2022, and Russian and Ukrainian troops continue to clash nearby, accusing each other of shelling around the station. The IAEA has been trying to set up a safety mechanism to prevent accidents.
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Grossi held talks with state nuclear power company Rosatom where safety at Zaporizhzhia was the main focus, the RIA news agency said, citing Rosatom. He also had discussions with the Russian defence and foreign ministries.
RIA reported that Grossi said the talks were "tense", without elaborating. An IAEA spokesperson denied Grossi had described the talks as tense.
Zaporizhzhia has lost its connection to all its external power lines eight times in the past 18 months, forcing it to rely on diesel generators for essential functions such as cooling the fuel in its reactors.
While one of its main power lines is currently functioning, the IAEA says the situation at the plant remains precarious.
One of the plant's six reactors, according to the IAEA, needs to be kept in a hot shutdown mode in order to produce steam required for nuclear safety, including the processing of liquid radioactive waste in storage tanks.
Ukraine said last year it feared the plant could face a shortage of water needed to keep it cool, after a giant dam was blown up down river, lowering the level of the adjacent reservoir.
Grossi inspected wells last month to determine if there was sufficient water for cooling, and welcomed a reduction in shelling around the site. Russian news agency TASS reported that Grossi had concluded the water supply was sufficient.
