Some scheduled trains were cancelled while others were stopped on Poland's 820 kilometres of railway.
Major malfunctions in electronic control systems have caused significant delays to Polish and Italian trains.
The technical glitches have halted a number of train routes that are being used to transport Ukrainian refugees to other European countries.
Polish government cybersecurity chief Janusz Cieszynski said an investigation had been launched into the malfunction.
The director of Poland’s PKP PLK railway company said that the sudden outage took place at 04:00 (CET) on Thursday and affected 19 out of Poland’s 33 control centres.
Some scheduled trains were cancelled while other traffic was left standing idly on Poland's 820 kilometres of railroads.
“Because the reach of the outage is almost nationwide, it is clear that some of the trains will not run at all,” Skubiszynski told reporters.
Poland’s railway was asking travellers to put off train journeys on Thursday as railway experts worked alongside the government’s cyber security team to gradually restore traffic. Some 10 control centres were back up and running around midday.
Skubiszynski said authorities were working to ensure that the outage does not hamper the travel plans of Ukrainian refugees, adding that special bus services were made available.
Poland has admitted nearly two million fleeing war following Russia's invasion of Ukraine on February 24.
In Italy, railway company TRENITALIA issued an alert saying that a control system outage had caused major problems along the key Rome-Florence line.
Many trains faced delays of up to two hours or have been cancelled due to the centralised issue, authorities said.
The problem was fixed by midday with train traffic gradually restored and delays shrinking, they added.
Infrastructure company Alstom said in a statement that Thursday’s delays on the Italian State Railway and in Poland were due to a computer bug in signalling software provided by Bombardier Transportation.
Alstrom said the malfunction was not the result of a cyberattack and that the safety of passengers was not at risk. A “mitigation plan” has proactively been put in place to minimise any potential disruption, the company said.