The Cabinet minister issued a direct plea to those embarking on three days of walkouts next week, stating they “risk striking yourselves out of a job”.
He also stated that the Government plans to introduce legislation to enable the use of agency workers on the railways during industrial action “if the strike drags on”.
Half of Britain’s rail lines will be closed during strikes on June 21, 23 and 25 by the Rail, Maritime and Transport union (RMT).
Transport for London (TfL) has also “strongly encouraged” people not to travel on London Underground on June 21 because of a 24-hour walkout by the RMT and Unite.
The disputes have flared over pay, jobs and conditions.
In a speech at a train depot in north London, Mr Shapps said the strikes would be “damaging” for railway workers and their families.
He told the audience: “These strikes are not only a bid to derail reforms that are critical to the network’s future, and designed to inflict damage at the worst possible time, they are also an incredible act of self-harm by the union leadership.”
He said the railway was “in a fight” as it was competing against remote working and other forms of public and private transport.
“We’re going to endanger the jobs of thousands of rail workers,” he claimed.
“The last thing the railway should be doing right now.
“It’s alienating its passengers and the freight customers with long and damaging strikes.”
Mr Shapps denied his comments on jobs were “a threat”, describing them as a “statement of the reality”.
He urged the unions to “join us on that journey” to reform the network.
“Don’t jeopardise the railways, and therefore by definition, the jobs that come from the railways,” he said.
In response, RMT general secretary Mick Lynch said: “The threats made by Grant Shapps today to railway workers’ livelihoods and their right to strike are disgraceful and will make RMT members even more fiercely determined to win this dispute.
“Instead of playing to the gallery for his own personal political ambitions, Mr Shapps needs to act like a pragmatic Transport Secretary who is willing to meet with the union and help us reach a negotiated settlement.”
Bully boy tactics will not wash with our union when the truth is our members are fighting for their jobs, pay and for a safe railway fit for the future
Manuel Cortes, TSSA
Transport Salaried Staffs’ Association leader Manuel Cortes said: “What we heard from the Transport Secretary looked very much like threats and intimidation of workers instead of constructive dialogue.
“Bully boy tactics will not wash with our union when the truth is our members are fighting for their jobs, pay and for a safe railway fit for the future.”
Mr Shapps claimed the Government has a “range of options” to respond to industrial action.
Enabling the use of agency workers would be “very much quicker” than requiring minimum service levels, he explained.
“People will be able to come where they have the appropriate level of skills, training and experience, and that is subject to a more straightforward secondary legislation process,” he said.
“If the strike drags on … then transferrable skills, sometimes called agency working, will be something which will become available as well in this particular dispute.”
Mr Shapps said season ticket holders would be paid “full compensation on strike days” next week, and he had “moved to help make that an automatic process”.