The two men had stashed about £10,000 of stolen goods in their vehicle following an overnight robbery spree in Arran when they boarded the Loch Tarbert vessel from Lochranza to Claonaig yesterday morning.
The pair attracted suspicion after arriving on the holiday island on Sunday evening and left soon afterwards. Their visit coincided with a number of raids on builders' vans in which tools worth thousands of pounds were stolen.
Police issued an alert to ferry operator Caledonian MacBrayne asking their staff to be on the lookout for anything suspicious.
The skipper of the Loch Tarbert raised the alarm with authorities after noticing a large cache of tools smuggled in the back of a van on board his boat.
As the vessel arrived to dock at Claonaig, however, the thieves realised the crew had found the stash of tools. The captain ordered the ramp be pulled up in an attempt to prevent the pair escaping the ship but, realising they were cornered, they two men leapt overboard into the shallow waters at the harbour and made their getaway on foot. Police searched their abandoned their car and found it loaded with stolen tools.
Captain Gavin Crawford said: "I received a message from our Brodick office to keep an eye open for any suspicious looking vehicles or passengers.
"And sure enough, there were two guys in a car on board who prompted us to take a closer look.
"They seemed calm as we took a look inside and found lots of tools and other building machinery.
"Some was covered up on the back seat, and the boot was jam-packed with other kit.
"The police were called and as we approached the slipway at Claonaig on Kintyre, I told the guys to stay put while the other traffic disembarked. They seemed at first to accept our command, but at the very last second they tried to drive off the ferry - but we managed to hoist up the ramp just in time to block them.
"However, they leapt out of the car and somehow squeezed round the edge of the ramp and jumped into the water before wading ashore and running up into the hills."
Police launched a helicopter to hunt for the men but they have yet to be caught.
Blackwaterfoot contractor John Robertson, who has owned a business on Arran for 50 years, said: "I want out to my van early in the morning ready for work - only to discover a whole lot of power tools, some of it hired, was gone.
"The value was at least £3,000 and probably more. This sort of thing seldom happens on Arran, so it came as a bit of a shock."
Arran police chief Allen Dodds said: "We received several reports from businesses on the island about missing gear.
"It seems these men had come to Arran on the main ferry from Ardrossan to Brodick on Sunday evening before targeting various locations.
"The only other route back to the mainland was on the smaller ferry from Lochranza at the north of the island and they boarded the first sailing at 8.15am.
"It seems they jumped off the vessel into waist-deep water and managed to get on to dry land and headed for rough ground.
"The Police Scotland helicopter was then detailed to join the search for the two suspects."
A Police Scotland spokesman said: "Following the theft of tools from a works van in Arran we were asked by Police to look out for a van carrying this type of load and our crew duly identified one on the MV Loch Tarbert travelling from Lochranza to Claonaig.
"Police were notified and, when the ferry arrived in Claonaig, the van tried to drive off but the ramp was raised to prevent it doing so.
"Two men then got out of the van and jumped into the water and ran up the slipway. The vehicle has been retained by police."