Union leaders said talks had failed to secure a fair deal for members while contractor Babcock paid "eye-watering" bonuses to top directors.
Unite said about 800 workers joined today's two-hour walk-out at the Faslane and Coulport naval bases on the Clyde this morning.
Further one-hour stoppages are planned from tomorrow as well as a work to rule and an overtime ban.
Unite national officer Ian Waddell said: "It's with a real sense of disappointment that our members are taking strike action for the first time in 42 years at the Clyde naval base.
"It's the culmination of months of fruitless discussions with Babcock over a fair pay rise for our members.
"They were initially offered a 1% pay rise in the same year that directors were given a 9% pay rise and shareholders enjoyed a 16% increase in their dividend.
"The company made £234 million in profit; they can easily afford a fair pay rise for our members. They have been very clear - all they are looking for is a 3% pay rise, no strings attached.
"To take that decision to go on strike when you've never done it in your working life is one of the most difficult decisions they will have had to make. But they delivered a very clear majority.
"There was a 95% Yes vote for strike action and they rejected the company's latest offer of a two-year deal with strings attached by 99% at a meeting last week.
"It's with a real sense of grim determination that they started strike action today."
Workers involved in today's action included catering staff, cleaners and employees responsible for fitting out boats and loading weapons, Unite said.
Mr Waddell said: "Nobody wants to be on strike, nobody wants to be making this sacrifice.
"These are dedicated, hard-working, skilled people who have demanding jobs.
"They want to be back at work, they don't want to be standing outside the base protesting about a derisory and insulting pay offer.
"All they are asking for is a fair share of the profits they have helped generate.
"Hopefully Babcock will respond to the protest today, pick up the phone and we can negotiate tomorrow as far as I am concerned."
Babcock has said it was ''surprised'' by Unite's decision, adding: ''We have engaged with our trades unions and carefully listened to their specific concerns.
''We have gone back to them with a new multi-year deal which significantly increases the consolidated pay element at their request and provides an opportunity for further reward.
"This means that, over the last three years, including the 2013 pay deal on offer, our industrial workforce would have received total consolidated pay increases of 8% as well as one-off payments totalling £1,150 - well above the UK national average pay increase during the same period.
''We believe this to be a fair and reasonable offer and are very disappointed by the decision to flatly refuse this offer and proceed with industrial action."