Improving Northern's train services are the Department for Transport's "number one performance priority", the government has said.
It comes amid widespread criticism of the company over cancellations, delays and the implementation of a new timetable earlier this week.
The department is also investigating whether Northern has breached its franchise agreement to run trains
The train operator has been contacted for a comment.
Transport Secretary Chris Grayling said plans to improve the company's performance had been submitted and he will be speaking to managers to discuss future steps.
"Improving the service for Northern customers is the number one performance priority for my department and we will work with the industry to keep disruption at a minimum," he said.
Measures in the plan include:
- Improving driver rostering to get more trains running now
- Increasing driver training on new routes to get more services on line as quickly as possible
- Additional contingency drivers and management presence at key locations in Manchester
- Putting extra peak services in the timetable along the Bolton corridor, including between Buckshaw and Manchester Victoria, and Preston and Manchester Oxford Road
Transport minister Jo Johnson said his department was assessing whether Northern's service on the Lakes line had breached its franchise agreement.
The company, which faces two days of strike action by staff later this week, has also apologised over the introduction of a new timetable on Sunday.
People and strategy director Richard Allen told BBC North West Tonight: "I'd like to say sorry and apologise to customers who've had to suffer cancellation and delays."
Many of the problems had been caused by delays in electrification work being carried out by Network Rail, he said.
"We are going to work to fix as many issues as we can over the next days and weeks," Mr Allen added.
Around one in every 10 trains due to be run by Northern has been cancelled since Sunday.
A spokeswoman for Network Rail said unforeseen problems delayed the engineering work but "we're seeing real progress towards the completion goal of December this year".
One Northern passenger, whose journey to work was affected by electrification of the rail line into Manchester, said he now intends to sue Northern in the small claims court.
Pat Condon, a compliance manager who commutes from Blackpool to Salford Crescent, said he has kept records showing more than 70% of his journeys have been delayed during the last six months.
The use of a replacement bus service also added 40 minutes to his journey time, yet there has been no compensation, Mr Condon said.
"What they don't do is communicate with their customers. We're often not told when trains will be cancelled. They're often rammed to the hilt with passengers. It's just a shocking service all round."
The mayor of Greater Manchester, Andy Burnham, who last week described Northern's service as "unacceptably poor" has again publicly criticised the company.
Mr Burnham posted on Twitter: "Last 14 days on Northern Rail. Full cancellations: 1,159. Part-cancellations: 1,048. Short trains: 529."
He also criticised the response from ministers, saying Northern commuters were "invisible" to them.
Liverpool City Region's Mayor Steve Rotherham has written to the company asking for an assurance "that my constituents are going to receive the service they expect and deserve".
"These sorts of failings are inconvenient for individuals, leading to missed appointments and late arrivals at work, and also have a damaging effect on the economy of our city region and the country as a whole," his letter said.
A spokeswoman for Transport for the North said they are "extremely disappointed and concerned with the inadequate performance of Northern".
"We have formally raised these concerns with Northern making it clear that we want more to be done to rectify the performance issues and to mitigate against impacts on passengers and for action to be taken immediately," she said.