A spate of drone attacks in Syria, Iraq, Saudi Arabia, Yemen and now Lebanon has raised the spectre of a new era of conflict in the region, due to the ability of stealth-like weapons to penetrate distant battlefields and hit closely guarded targets.

Drone warfare has become an instrumental factor in the escalating conflict between Israel and Iran, now being fought over both sides of the Israeli border and in skies across the region.

Small, cheap to produce and capable of evading radar systems, drones have been a centrepiece of the Israeli military’s arsenal for years – primarily in its operations over Gaza.

Iran has also begun deploying the unmanned, remotely piloted machines in clashes with Israel. Tehran has long used proxies in such actions but is now increasingly carrying them out itself. All sides see the technology as having surgical qualities.

Israeli officials have told European diplomats the two drones which crashed in Beirut on Sunday were sent from Israel to disrupt efforts by Hezbollah to fit advanced guidance systems to rudimentary rockets, sources have revealed.

The drones fell in the Lebanese capital’s southern suburbs, a stronghold of the militant group, which retrieved the damaged machines and has since claimed they were fitted with about five kilograms of plastic explosives.

Two western diplomats said the unusual operation may have been an assassination attempt, or an attempt to destroy a site vital to Hezbollah’s ability to retrofit its rocket arsenal. Either theory suggests the attack was an attempt to deter efforts to fit guidance systems to missiles.

On Wednesday evening the Lebanese army said it opened fire on two of three Israeli drones that breached Lebanese airspace in the south of the country near the border, and all three returned to Israeli airspace. They first entered Lebanese airspace at 7.35pm and returned to Israel after shots were fired, the army’s statement said. A second drone returned to Israel without being fired at. The army fired at a third one, which also returned back to Israel, it said.

The development comes as Shia militants in Iraq claimed that Israel has used drones launched from Azerbaijan to attack targets in the north and centre of the country – areas which regional officials say have become transit hubs for weapons being sent to Iranian positions near Israel. US, Iranian and Iraqi officials say that since mid-July Israel has flown advanced machines fitted with missiles hundreds of miles into Iraq to attack five targets linked to Iranian proxies operating there.

Abu Mahdi al-Muhandis, an Iranian ally and the deputy leader of Iraq’s Popular Mobilisation Units (PMU), a network of militias that coalesced to fight Islamic State, said: “We have accurate and confirmed information that this year the Americans introduced four Israeli drones via Azerbaijan to operate within the US fleet to carry out flights and target Iraqi military bases.”

Muhandis is also the leader of the Shia militia, Kata’ib Hezbollah, one of Iran’s most influential proxies in Iraq, which has taken a lead role in safeguarding a corridor of Iranian influence from Tehran to the Mediterranean coast. Securing a route through western Iraq and eastern Syria has been a goal of Iran’s leaders over the past three years, particularly as Islamic State’s presence has withered.

Regional officials say the establishment of such a corridor would entrench Iran’s influence in the centre of the region..

“The Iraqi government has no control over its borders,” said Iraqi researcher and government adviser, Hisham al-Hashimi. “The government turns a blind eye to the operations that these groups run on the border because they played a significant role in the fight against Isis.

“The main concern is the possibility of the transportation of missiles from Tehran to Beirut that will target and threaten the security of Israel.”

Muhandis said the apparent Israeli strikes – the latest of which killed two members of Kata’ib Hezbollah near the Iraqi border town of al-Bukamal on Sunday – had been carried out with US support.

“Recently they surveyed our bases instead of Isis and collected information and data on the bases and weapon warehouses,” he said. “The targeting of PMU headquarters is clear evidence of the full control of the US military over Iraqi airspace.

Israeli officials have repeatedly claimed a consolidated Iranian presence near Israel’s borders would be intolerable. They have also insisted that fitting guidance systems to the thousands of rockets in Hezbollah’s arsenal poses an existential threat to the country.

An Israeli military spokesman, Lt Col Jonathan Conricus said Iran’s efforts appeared to have stalled.

“The Iranians are nowhere near where they had planned to be at this stage,” he said. “They are far behind, in terms of quantity of troops and the facilities and the capabilities that they intended to have in place in Syria, and that they tried to equip Hezbollah with.

“The negative side is they are still in Syria, they are still trying to entrench themselves, they are still spreading violence across the region – whether it be Yemen, Lebanon, Iraq, Syria, the Gulf area and other places. When it comes to our perspective, we see that they are still trying to establish themselves in Syria with offensive capabilities.

“There is no other explanation for what the Iranians are doing in Syria, what the Iranian Revolutionary Guards Quds Force under [senior commander] Qassem Suleimani is doing in Syria, than to threaten Israel and to have military capabilities capable of striking Israel.”

Sources at senior levels of the Iraqi government say one of the targets allegedly hit by Israel, in the town of Amerli in July was a convoy of refrigerated trucks, which contained medium-range guided missiles.

“They were going to be sent overland. The Iranians still don’t know where their final route to Syria is going to be. Nothing is really working so far, so they are trying as many routes as possible, and hoping that one eventually becomes clear.”