As many as 8% of Transport for Wales (TfW) trains have been overcrowded since late July despite restrictions on travel, a leaked document shows.
From the start of lockdown in March until Monday, only essential travel was allowed on public transport as trains operated at 20% capacity.
But an internal document seen by the BBC reveals challenges faced by staff.
TfW said safety was a "top priority", adding 500 people were refused travel last week.
Incidents described in the report, based on the accounts of conductors, include a 09:23 Holyhead to Birmingham two-carriage train which was carrying 67 passengers at Llandudno Junction, but then had 89 by the time it left Flint.
Many of the incidents involved trains travelling to and from Barry Island, with one service from Pontypridd carrying 99 passengers by the time it reached Cogan.
An 08:40 train to Cardiff Central left Ebbw Vale Town with 56 passengers, including 30 children, mainly travelling to Barry Island.
And a 12:31 Manchester Piccadilly to Carmarthen train with three carriages had 70 passengers when it reached Llanelli.
TfW said that, on average, it is currently operating about 689 services every day, and that between 5% and 8% of trains have exceeded the permitted capacity.
"The number of people (or capacity) we can safely have on board is worked out using a worst case scenario, aimed at keeping everyone 2m apart," a TfW spokesman said.
"In reality, families and those from the same household can sit together, which effectively raises the numbers over the capacity indicator allocated for each unit (without necessarily making it less safe).
"During the hot weather, we have seen more people ignoring the essential travel message."
People are still required to wear face coverings on public transport in Wales, although there are some exceptions.