The train company admitted its profits for 20112/12 were “marginally” higher than the previous year’s £20.4 million.
Scottish Labour and passenger groups have criticised the fare hikes, and union leaders branded the increase “bonkers” last week.
Full details of the firm’s profits are still to be made public.
ScotRail announced it would put up fares in the Strathclyde region by 4.2% next year, one point above inflation.
Train ticket prices in the rest of Scotland are also expected to rise.
Richard Baker, transport spokesman for Scottish Labour, said: “For ScotRail to increase profits while the public suffer ever-increasing fares suggests that something is remiss.
“It’s essential that nministers engage with ScotRail to look again at these latest fare hikes.”
David Sidebottom, director of consumer body Passenger Focus said: “Passengers are less concerned about ScotRail’s profits than they are about value-for-money rail fares on punctual, reliable and frequent train services.
“However, an increase in ScotRail’s profits might set passengers wondering why fares need to go up as much as they inevitable will.”
The price increase is based on the July retail price index of 3.2%.
Regulated fares, which cover journeys in Strathclyde, season tickets and off-peak returns will be affected.
The cost of an Edinburgh-Glasgow season ticket is expected to go beyond £3,500 from its current level of £3,380.
Rail fares in the rest of Scotland have increased by an averageof 5% in recent years, though ScotRail insists no decision has been taken as yet.
The company’s 10-year franchise deal come up for renewal in 2014.
It has consistently increased fares by the maximum allowed but says this is vital to covering costs of improving services.
The FirstGroup company received £305million in public subsidies from Holyrood last year.
The full report on ScotRail’s income is due on November.
Reacting to the price hikes announced on Tuesday, National Union of Rail, Maritime and Transport Workers organiser Mick Hogg said: “Higher fares mean bigger profits for the private companies, staff and service cuts, the closure of ticket offices, cuts to terms and conditions, and potential job losses.”
He added: “What we want to see in an ideal world is the renationalisation of the railways, because we don’t see any sense in this madness.
“It’s absolutely bonkers as far as we are concerned, particularly with the austerity cuts that are taking place, poverty and people facing job losses.”
A ScotRail spokeswoman said: “Profits were up marginally in the year ending March 2012.
“Full accounts will be published as scheduled later this year.”