A man was arrested after police were called at 1212 BST to Southampton docks where the vessel has been berthed since Wednesday as part of a five-day visit.
The BBC's Jonathan Beale understands that a crew member shot two of his crew mates before being overpowered.
A police spokeswoman said the incident is not linked to terrorism.
She said there is no public safety risk and the area is sealed off.
BBC News understands the arrested man was handed over to Hampshire police by Ministry of Defence police.
Brian Cedar, who lives in Hythe marina, said: "I saw at least six people carry a stretcher off the gangway into a waiting ambulance.
"There were a couple of forensic people who have now left.
"If you can have a shooting like this on a nuclear submarine it is worrying."
The area around the docks has been sealed off by officers from Hampshire police.
The 97m-long (318ft) HMS Astute, the UK's newest and largest nuclear submarine, is based at the Faslane Naval Base on the Clyde.
HMS Astute is currently berthed in Southampton as part of a five-day visitIt ran aground on a shingle bank between the Scottish mainland and the Isle of Skye in October last year and remained marooned for several hours.
HMS Astute was named and launched by the Duchess of Cornwall in June 2007 before being welcomed into the Royal Navy in August last year at a commissioning ceremony at Faslane Naval Base on the Clyde.
The submarine weighs 7,800 tonnes, equivalent to nearly 1,000 double-decker buses, and is almost 100 metres (328ft) long.
Its Spearfish torpedoes and Tomahawk cruise missiles are capable of delivering pinpoint strikes from 2,000km (1,240 miles) with conventional weapons.
The submarine's nuclear reactor means it does not need refuelling and it makes its own air and water, enabling it to circumnavigate the globe without needing to surface.
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