Irish Rail has said there have been teething problems, including a lack of capacity in some areas, following the introduction of the new higher-frequency Dart service in Dublin this week.
The company said it would be in contact with the National Transport Authority to try to deal with these issues in the coming days.
Areas affected by capacity problems included northside stations close to the city, such as Killester and Clontarf Road, where Dart services were often full with commuters from the outer suburbs, the company said.
Irish Rail said longer journey times, which some passengers had complained about on social media, amounted to two or three minutes extra and had been flagged in advance in the revised timetable, which came into effect this week.
The company said this was due to trying to get more trains through the city centre rail route.
As part of the move to introduce a 10-minute Dart frequency, some northern line commuter services are no longer stopping at Portmarnock or Clongriffin. This has led to overcrowding on the remaining services, particularly closer to the city centre.
Irish Rail said south Dublin services were not affected.
Shorter trains
Solidarity councillor for Dublin city Michael O'Brien said on Tuesday that the rail company had reduced the capacity on existing Dart services as part of the move to increase the frequency.
"Irish Rail have sold these changes as a total positive in the sense that Darts will arrive every 10 minutes from Howth Junction to Bray and back."
“However, instead of investing in the necessary extra rolling stock in line with the increased frequency, they have simply lopped off carriages from the pre-existing services thus leaving commuters at peak times with shorter trains and resultant overcrowding.
"On top of this, commuters in Portmarnock have lost their three morning peak-time northern suburban services, leaving those passengers having to pile on to the available Malahide Darts. By the time these Darts arrive at their third stop in Clongriffin they are full, and the situation worsens as these journey progress towards the city centre."
A spokeswoman for Irish Rail said in some circumstances the number of carriages on particular trains had been reduced as part of the new changes. However, she said the company believed this was balanced by the provision of additional services.