Irish Rail says a two metre distancing rule "no longer applies on public transport", while services run at 50% capacity.
However the company has apologised for a lack of social distancing on one of their trains on Sunday.
A photo has circulated on social media showing apparent overcrowding on the Galway to Dublin train.
It shows a crowd of people sitting on the floor of the train with little to no social distancing.
Barry Kenny from Irish Rail told Newstalk Breakfast: "Well firstly obviously sorry to people who travelled on that service.
"Our service at the moment are operating 50% of capacity - so while in a normal circumstance there would have been obviously sufficient seating for everybody... 50% of the seats are currently blocked off.
50% of the seats are marked off so that people can socially distance - yet every carriage corridor looks like this. Impossible to get to the toilet without being on top of one & other. I don’t mean to sound negative - but this is not right @IrishRail @MichealMartinTD pic.twitter.com/hGhP43Fj5l
— Holly Carpenter (@Holly0910) July 19, 2020
"Right through this crisis and obviously as the economy has been re-opening on a daily basis we're monitoring demand, we're looking at capacity, we're looking at train sizes, we're looking at train frequency.
"In the overwhelming majority of cases we are meeting that demand within that 50% capacity.
"That obviously wasn't the case on this service yesterday... and we will obviously then look at that schedule for next weekend again to see do we need an extra train there, do we need additional carriages?
"I would say the advance booking didn't necessarily indicate that we would have that issue, but with open tickets as well unfortunately it did materialise."
"The two metre distancing rule no longer applies on public transport - public transport now operates at 50% capacity.
"And in line with that [there are] face coverings.
"That's why face coverings was introduced, because obviously it's a difficult environment in any country to all times maintain social distancing but to allow us to do more of a job in terms of facilitating the economy re-opening.
"So 50% capacity is what applies there.
"What we have is the window seats are available for use, the aisle seats are not.
"So in circumstances where there is some limited standing, it means that the aisle can be available.
"It appears that a group may have congregated there, but I wouldn't put blame on the people involved."
"When we get to September, when we anticipate more demand, that's obviously going to be a challenge - not just for us but for all public transport operators.
"But the key for customers is to ensure that they do have those face coverings, because at a time during journeys between getting on and off it may not always be easy to maintain that distancing".