Despite the poorer service, however, Transport Minister Doris Leuthard announced on Sunday that fare hikes are to be expected in 2017.
Only 87.5 percent of rail travellers on the state-owned network arrived on time in trips taken last year, down from 88 percent in 2012, SBB confirmed the same day.
The percentage of trains on time was even higher in 2011, when 89.8 percent arrived as scheduled.
The main reason for the fall-down in performance was construction work on lines crossing the centre of Zurich, which had a domino effect on the whole network, SBB said, according to a report from SDA news agency.
To evaluate punctuality, the SBB considers that any trains arriving three minutes or more after their scheduled arrival time are late.
The criteria is the strictest in Europe, railway spokeswoman Franziska Frey told SDA.
SBB will released more detailed data on its performance for 2013 in March when it is scheduled to release results for the year.
The opening of the “diameter line” through Zurich for local trains this summer and to long distance trains in December is expected to improve overall punctuality this year.
Meanwhile, Leuthard, the transport minister, told weekly newspaper SonntagsZeitung that higher ticket prices were expected from 2017.
She said this would be the case even if Swiss voters, as expected, approve a 6.4-billion-franc ($7.09-billion) rail infrastructure package.
Leuthard also noted the federal government will present a mobility pricing proposal that would make travel at peak times more expensive.
Even with increases in capacity, she said that some passengers will still have to stand on routes that are already overcrowded, something about which she felt “uncomfortable”.
Such routes include Bern-Zurich-Saint Gallen; Zug-Lucerne; Basel-Liestal; and Geneva-Lausanne.