NEW DELHI - Decrypted communications between Indian Mujahideen (IM) and al Qaeda and testimony from suspects have triggered alarm among intelligence officials in New Delhi: the groups appear to be working together to launch major attacks in the region.

The officials told Reuters that plots they had uncovered included the kidnapping of foreigners and turning India into a "Syria and Iraq where violence is continuously happening". Allegiances between militant groups can be murky and fleeting, and providing concrete proof of operational ties is notoriously difficult.

But Indian security agencies said evidence they had gathered pointed to growing ties between al Qaeda and IM, a home-grown movement hitherto known for low-level attacks on local targets using relatively crude weapons like pressure cooker bombs.

Weeks after al Qaeda announced the formation of a South Asia wing to strike across the subcontinent, agencies said they had discovered IM members were training with al Qaeda and other groups in Pakistan and Afghanistan for major attacks.

"The thing we are looking for is how al Qaeda/ISIS tie up with local groups, especially as the drawdown takes place in Afghanistan," said Sharad Kumar, head of the NIA (National Investigation Agency), the country's main counter-terrorism arm. ISIS, also known as Islamic State, has carved out swathes of territory in Iraq and Syria, but its influence over militant groups in South Asia is believed to be limited so far.

Al Qaeda is deeply entrenched, however, with leader Ayman al-Zawahri believed to be hiding near the Afghan-Pakistan border and its militants fighting NATO forces in Afghanistan.

 Foreign combat troops are due to withdraw at the end of the year.

Some members of IM are already fighting alongside al Qaeda in Afghanistan, according to an Indian government chargesheet against 11 suspected members of the group alleged to have plotted attacks in India.

The worry is that more battle hardened fighters could now turn their sights on their homeland.

Others have enlisted with al Qaeda to try to carry out kidnappings of Jews in India and Nepal to secure the release of Pakistani Aafia Siddiqui, a neuroscientist jailed for 86 years in the United States for attempting to kill US soldiers in Afghanistan.

Siddiqui is a cause-celebre among global militant groups, including Islamic State, which proposed swapping her for American journalist James Foley before executing him when its demands were not met.

IM has also been urged by al Qaeda to open a base in Myanmar to avenge attacks on Rohingya Muslims, said the chargesheet prepared by the NIA, which has gathered hundreds of pieces of evidence of Internet conversations and meetings between militants in India, Pakistan and Afghanistan.

"This is an outdated story. It does not serve any purpose for Pakistan to support such groups," said a senior intelligence official in Islamabad, requesting anonymity as he was not authorised to speak to the media about the issue.

"These terrorists are openly attacking us, the army, innocent civilians, everyone here is a target," he told Reuters. "Why would they do so if we were helping them in any way?"

A spokesman issued a direct warning to India's nationalist prime minister, Narendra Modi, saying his group would avenge the killings of Muslims in the disputed region of Kashmir and the Indian state of Gujarat, which Modi governed from 2001 to 2014.

Two Indian naval warships were abruptly ordered back to sea on Tuesday, a day after they docked at Kolkata port after intelligence agencies issued a terror alert.

On Wednesday the warning was widened to the neighbouring Haldia port, the site of a huge petrochemicals complex.

Kolkata Port Trust deputy chairman Manish Jain, who is also in charge of the Haldia port complex, said security had been enhanced several times over in both the ports.