Seven times world champion Schumacher, who hopes to re-energise his title hopes with a win in Montreal, was 15th quickest in the afternoon after posting the fourth best time in the morning.
"They (Ferrari) were not 100 percent today, tomorrow they will look competitive," said Renault's Alonso.
"I think maybe today they were a little too slow, on purpose maybe. I think maybe today Ferrari was playing," he told reporters.
"I think tomorrow for qualifying Ferrari will be one big opponent."
BMW Sauber's test driver Robert Kubica posted the quickest time on Friday with a lap of one minute 16.390 seconds on a grey overcast morning at the Circuit Gilles Villeneuve.
The promising Pole, who will not race on Sunday, returned under brighter skies in the afternoon to clock 1:16.965 ahead of Alonso's Renault.
The 24-year-old Spaniard, chasing a fourth consecutive win, did not take part in the morning session but quickly came to grips with the tight 4.3-km circuit that has not been kind to him in the past.
In four starts there, he has finished just once.
GREAT OPPORTUNITY
Alonso made an uncharacteristic error in last year's race and hit the concrete wall at the exit of the final chicane while in the lead. It was his last failure to finish and he has now been on the podium for 14 races in a row.
"I never get on the podium here and in Canada and never finish in Indianapolis, these two races have been quite bad for me in the past, so it's time to change it," said Alonso.
"I think this year I have a great opportunity with a fantastic car and I'm really focussed on doing a good job.
"The car has been competitive always, we just need a race with no problems, no mistakes and this Sunday will be the opportunity."
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Trailing Alonso by 23 points in the drivers standings, Schumacher's hopes of a record eighth drivers' crown may well hinge on how well he performs on Formula One's two-race swing through North America.
The 37-year-old German has won seven times before in Canada.
"As usual on the first day here in Montreal, the track is very slippery and we in particular suffered with quite a significant loss of grip," said Schumacher.
"We were not quick enough and we have to study the data to see how to improve.
"Obviously the gap separating us from our rivals today is a big one, but we know the situation can change rapidly."
