The team sent series leader Lewis Hamilton and his closest competitor Nico Rosberg out in the rain during practice at the Canadian Grand Prix on Friday, only to have Hamilton aquaplane into a tire wall and then have his car damaged by the crane that lifted it off the track.
Team boss Paddy Lowe said the damage to the rear end, which came when the car swung into the crane, was "nothing serious."
Hamilton had already set the fastest lap of the day of one minute 15.988 seconds on the 4.361-kilometre Circuit Gilles Villeneuve, but Rosberg was only fourth behind the team's main threat for the race, the Ferraris driven by Sebastian Vettel and Kimi Raikkonen.
A third practice is set for Saturday ahead of qualifying. The 70-lap race is on Sunday.
Light rain started about 34 minutes into the second 90-minute practice of the day and all the cars went to the garages. A moment later, the two Mercedes went out again. Almost immediately, the rain came down in a deluge.
Hamilton couldn't stop while coming down a flooded straight into a hairpin turn, and he coasted into a tire barrier.
Lowe said he hoped the drivers would get two or three practice starts in before the rain intensified.
"Unfortunately the conditions worsened quicker than we anticipated and the conditions caught Lewis out in an unfortunate manner," he said. "But we'll get it sorted. It should be all fine."
Mercedes is still smarting from a gaffe at Monaco, when Hamilton was deprived of an almost certain victory we he was called in for a tire change while the race was under a safety car. Rosberg ended up with his second straight victory to move only 10 points back in driver standings.
Lowe said the team made changes to its software and the duties of team members to ensure it won't happen again, and said reports the team did not take the incident seriously were wrong.
"Formula One is a complex business. There are a lot of things to get right and most of the time we do that," he said.
Hamilton did not appear concerned.
"It's been a good day," he said. "It wasn't my call to go out.
"We collectively don't think it was the best call to go out but, at the end of the day, it doesn't affect our running."
The huge crowds lining the island track got soaked in the downpour.
While the Mercedes duo dominated the morning session, Ferrari charged back in the afternoon with Vettel second quickest at 1:16.304 and Raikkonen third at 1:16.310.
Ferrari made improvements to their cars going into the Canadian GP and hope to challenge Mercedes, which has won five of the first six races this season.
"Ferrari seemed to be quick," said Rosberg. "That's a massive threat at the moment, but let's see where they are exactly."
Raikkonen was also cautious when asked if Ferrari was ready to challenge.
"It's hard to say," he said. "We didn't get so much running today because of the weather issues, but we'll try to improve things and we'll see where we are."
It was a good day for Lotus as Pastor Maldonado was fifth and Romain Grosjean seventh. Williams and Red Bull also placed two cars in the top 10.
"It's going to be closer than expected this weekend," said Red Bull's Daniel Ricciardo, who got his first F1 win here last year.