In concluding remarks following talks at the Russian strongman's Black Sea residence in Sochi, the two leaders gave little away about their closed-door meeting.
But Putin's official spokesman Dmitry Peskov confirmed that Israel had raised the issue and that Russia defended the arms deliveries.
"The issue was raised. The Russian Federation presented its arguments, which are well known," Russia's Interfax news agency quoted Peskov as saying.
Russia's position "was heard," Peskov added, without providing further details except to say that the meeting went "well".
Israel wants Russia to halt supplies of the formidable S-300 missiles that would severely complicate any future air attacks against the regime of Syrian President Bashar al-Assad.
Netanyahu himself did not mention the sensitive weapons issue in public but Putin warned against any destabilising moves in the Middle East, days after Israeli forces launched air strikes against regime targets in Syria.
"In this crucial period, it is especially important to avoid any moves that can shake the situation," Putin said in televised remarks.
Netanyahu meanwhile stressed that it was his country's task to defend its citizens.
The Israeli prime minister added: "Together we are trying to find ways to strengthen stability and security. It's important both for you and us."
The agenda for Tuesday's meeting had some parallels to a trip Netanyahu made to Moscow in September 2009 for Kremlin talks deemed so sensitive that the visit was kept secret at the time.
According to Israeli media, Netanyahu is believed on that trip to have raised fears about a Russian plan to deliver S-300s to Iran that Moscow decided in the end not to fulfil.
Viktor Kremenyuk, deputy director of the USA and Canada Institute, suggested that Netanyahu would warn Putin during the current visit that his airforce would target the S-300s should the Kremlin decide to deliver the arms to Syria.
"Indirectly, he is letting him know that Israel would destroy the S-300s when they get delivered and start being assembled," he told AFP ahead of the meeting.
Russian Foreign Minister Sergei Lavrov said last week that Moscow was "completing" supplies of equipment to Syria agreed under previous contracts.
According to the Wall Street Journal, citing an Israeli intelligence report, the 2010 contract with Syria includes six launchers and 144 missiles, each with a range of 125 miles (200 kilometres).
Netanyahu was just the latest world leader to beat a path to Putin's door for talks on Syria in recent days, after US Secretary of State John Kerry and British Prime Minister David Cameron met him last week.
In the wake of the talks with Netanyahu at Putin's vacation residence in the southern resort of Sochi, UN Secretary General Ban Ki-moon is also due meet Putin in Russia on Friday.
Cameron said on Monday after talks with US President Barack Obama that London and Moscow had found "common ground" on the crisis.
Obama was more cautious however, saying there were "lingering suspicions between Russia and other members of the G8 and or the West".
Particular hope has focused on a Russian-American agreement to work towards convening a peace conference on Syria.
The conference is likely to be held in early June, said a State Department spokeswoman on Monday.
Jordan's foreign ministry said on Tuesday Amman would host a meeting of the largely anti-Assad "Friends of Syria" group of Western and Arab states that is likely to discuss the conference.
Upping the stakes, Kerry said in Sweden that Syria's opposition would receive additional assistance if Assad refused to attend the proposed peace conference in person.
The latest push to try to find an end to the slaughter in Syria comes as the war is taking a turn for the worse amid reports that the Assad regime is starting to win back territory.
The Syrian Observatory for Human Rights said earlier Tuesday that at least 94,000 people had now been killed in more than two years conflict, revising up a previous toll.
A gruesome video also surfaced in which a Syrian rebel fighter is shown cutting out the heart of a regime soldier.