A second day of rail strikes is under way after talks between the RMT union and railway employers broke down.
The RMT accused Transport Secretary Grant Shapps of "wrecking" negotiations by refusing to allow Network Rail to withdraw redundancy threats.
Mr Shapps called the claim "a total lie", adding the union was solely to blame for the "massive disruption".
Thursday's strike is set to have a similar impact as Tuesday's, with just 20% of services running.
Millions were affected on Tuesday at the start of the largest strike in decades. Another walkout is due on Saturday.
The second day of strikes will see half of the rail network in Britain closed.
In London, there are no strikes taking place on the Tube network, though operator TFL has warned of disruption to some services, including the London Overground.
It comes as the Met Office issued a yellow weather warning for thunderstorms across much of southern England, potentially adding to disruption.
The breakdown in talks between the RMT and rail companies led to recriminations between the union and the government.
Mick Lynch, general secretary of the Rail, Maritime and Transport (RMT) workers' union, claimed Transport Secretary Grant Shapps had "wrecked" negotiations by not allowing Network Rail to withdraw its letter threatening redundancy for 2,900 of our members.
Mr Shapps called the claim "a total lie", saying he had no involvement in the letter.
The Department of Transport has said the rail industry is leading the negotiations, but a contract seen by the BBC says that train operating companies' handling of strike action is "subject to the secretary of state's direction".
A Network Rail source told the BBC little progress was made in Wednesday's talks, with the union's position appearing to have hardened. No new pay offer was made.
Both sides in this dispute insist that in recent days they had thought progress was being made. But Wednesday's talks again ended without an agreement.
As things stand, a deal to avert the third strike going ahead on Saturday isn't looking particularly likely.
The RMT union says that in talks, it asked Network Rail to withdraw Monday's letter about pressing ahead with a formal consultation over changes to working practices in maintenance teams - which would entail redundancies.
A source at Network Rail, which maintains and operates the tracks, described this as a "red herring". They insisted the letter could be ripped up if the union would properly negotiate on the reforms.
There wasn't a new pay offer yesterday. So far, both train companies and Network Rail have offered an unconditional 2%, with a further 1% conditional on accepting changes they say are necessary to modernise ways of working.
Meanwhile, passengers face another day of travel misery.
More rail commuters can switch to working from home than would have been possible in the past, but not everyone has that option and many plans will be disrupted.
The RMT is calling for a pay rise of at least 7% to offset the cost of living crisis, as inflation hits 9.1% and is forecast to reach 11% in the autumn.
Employers have offered a maximum of 3%, on condition that the union accepts new working practices.
But rail employers said they had suffered a loss of income, with passenger numbers only at 80% of pre-pandemic levels.
The Rail Delivery Group, which represents train operating companies, said it wanted to give "a fair deal on pay while taking no more than its fair share from taxpayers", which meant modernising the railway to attract passengers back.
On Tuesday, the prime minister urged the country to "stay the course" and resist high pay rises he said could further fuel inflation.
On Tuesday about 40,000 RMT members working for Network Rail walked out, leaving many parts of the country with no rail service at all.
Disruption continued on Wednesday, with only about 60% of normal services running.
At Prime Minister's Questions on Wednesday, Labour leader Sir Keir Starmer accused Mr Johnson and the transport secretary of not "lifting a finger" to stop the strikes.
Mr Johnson responded that the government was doing "everything we can to prevent these strikes" and it was up to the railway companies to negotiate.
Meanwhile, the government is planning to introduce a new law this week to make it legal for employers to bring in agency staff to replace striking workers - but it will not impact the planned rail strikes on Thursday and Saturday.
Additional reporting by Katy Austin and Jessica Sherwood
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