The rail regulator has said Network Rail must improve its performance or face a fine.
The Office of Rail and Road (ORR) said punctuality and reliability fell to their lowest levels since 2014 between April and mid October this year.
The ORR said Network Rail's performance has been affected by factors such as extreme weather and the problems in implementing the botched timetable upgrade in May.
The formal action is the first time in a decade that the ORR has issued an order against Network Rail. It said the order was because the publicly-owned body may have breached the first condition of its licence regarding management.
As part of the action Network Rail is required to work more closely with train operators to address the concerns raised in the report and provide regular updates on its improvements.
It has also ordered Network Rail to produce its own report into how it plans to recover services after incidents on its network by February next year.
ORR's chief executive, John Larkinson said: "Today's decision is a clear demonstration of ORR's approach to how we will hold Network Rail to account.
"Passengers and freight customers rely on Network Rail for punctual and reliable train services and the evidence we have collected suggests to us that Network Rail is failing to take all reasonable steps to effectively manage performance and recover from incidents on its network. This is a capability issue which must be addressed urgently," he said.
Andrew Haines, Network Rail chief executive, said: "We know that train performance has not been what our passengers deserve. We have let them down and we take responsibility for the part we have played in poor train service reliability.
"Network Rail is fully committed to leading the industry back to higher levels of performance both through our own measures and actions and by working closely with our industry partners."
Separately, the Department for Transport is expected to soon announce how it will punish Govia Thameslink Railway (GTR) to account for the chaotic introduction of a new timetable, with more services, in May following weeks of negotiations.
The formal action comes as the ORR ramps up its efforts to hold Network Rail to account. Yesterday it opened a consultation for new policies that could see fines against Network Rail funded by management bonuses rather than from resources that would otherwise be used on the rail network.