The Honda rider was one of two riders alongside Qatar GP winner Enea Bastianini to crash towards the end of a sweltering FP2 session on the opening day of running at the new Mandalika International Street Circuit.
Marquez slid off his RC213V at Turn 11 while on a hot lap on soft rubber as he sought a provisional qualifying Q2 place.
But the crash left him down in 22nd on the combined order and facing the Q1 battle on Saturday as rain is forecast to hit FP3.
“I crashed and [that] was not the time for crashing,” Marquez said on Friday. "But when you push on the single lap sometimes it can happen.
“It’s true that overall for the day I’m happy, but with that crash we cannot be happy because we are out of top 10 and that was the target.
“But anyway, now it’s time to pray for a dry FP3 and try to be in the top 10.”
Marquez’s team-mate Pol Espargaro topped FP1 at Mandalika on Friday, but also sits in a provisional Q1 place in 19th after a front brake issue thwarted his time attack effort in FP2.
“I had no front brake in the last run when I put the [new] tyres,” Espargaro explained. “So, I was especially angry because if tomorrow rains we are not in Q2.
“So, it was the only opportunity to get into Q2. Also, I had a good chance to be in the top three because we have good speed here. But suddenly the front brake stopped braking. We had an issue there.
“We have many parts on the bike, this can happen. It’s a technical issue and hopefully tomorrow we can solve it.”
Despite his FP2 crash, Marquez said he felt as if Honda had made strides in bringing the set-up of the radically overhauled RC213V closer to suiting his style, having admitted on Thursday ahead of the Indonesia round that he was still uncertain of where the limit of the front-end was.
“We change a little bit already the set-up to my direction in FP2, and I started to feel better and better,” Marquez added.
“It’s true in the last run we were riding a different bike again. But it’s not bad. Looks like that front contact, front confidence is coming better.”
A key change to the tyres this weekend has been the reintroduction of a stiffer casing in the rear Michelin options last used in Thailand in 2018.
The alternate casing has been brought to cope with the extreme heat at Mandalika, but most have noted that it has generally offered less grip than the tyres used at the pre-season test in Indonesia last month.
Espargaro spent 2021 battling a lack of rear grip on the Honda, but says the old casing hasn’t caused him many issued.
“I’m not feeling it so much, actually,” when asked about the different tyre casing. “For sure it’s [the grip] less than the test, but I feel like we are not having more troubles than the others.
“I feel we are in the same level than the others.
“In the morning, with the track very dirty, I was with the medium tyre and I was able to set up the fastest lap time.
“And also this afternoon I was around top five, so I feel OK. Honestly the bike feels very good in both tyres.”
