The Syrian government-run media blamed the strikes on the US -led coalition fighting the Islamic State group.
"Whether Iranian forces or Hezbollah withdraw or stay in Syria is not up for discussion because it's the (business) of the Syrian government", Lebanon's al-Mayadeen TV quoted Syria's Mekdad as saying on Wednesday.
The Britain-based Syrian Observatory for Human Rights, which tracks the war through a network of activists on the ground, said the fatalities were not Syrian nationals but foreign fighters.
The attack sparked large explosions, which were heard throughout the area.
Russian Federation and Iran support the government of Syrian President Bashar al-Assad in the complex Syrian conflict, which is now in its eighth year.
Eastern Syria was mostly held by Islamic State until previous year, when two rival campaigns, one by the Syrian army backed by Russia, Iran and Hezbollah, the other by Kurdish and Arab militias backed by the USA coalition, took most of its land.
Israeli Prime Minister Benjamin Netanyahu has said Israel will not allow Iran to threaten Israel from Syria.
It added in another tweet that the U.S. coalition targeted T2, an energy installation located "near the border with Iraq and about 60 miles west of the Euphrates river where the coalition is backing ground forces against Islamic State", according to Reuters.
The Israeli military refused to comment on the strike.
The US-led coalition against ISIS in Syria on Thursday denied carrying out any overnight attacks against Assad regime targets.
Western powers blamed Assad and Putin for the attack and have since flown bombers over the country where they have carried out a series of raids.