The triple Formula One world champion will line up in fourth place for Mercedes, with team mate Valtteri Bottas third and behind the pole-sitting championship leader Sebastian Vettel and Kimi Raikkonen.
"It's not every weekend that goes perfectly smoothly," said Hamilton, the winner in China who has a hard road ahead of him on Sunday to prevent Vettel increasing his seven-point advantage.
Hamilton had struggled in practice to get the tyres up to temperature, despite warm conditions at a track that has favoured Mercedes ever since its debut in 2014.
"We worked towards improving the car but generally it got worse and worse... I think it was just the balance that we had," added the Briton.
"Over tonight we'll do some studying and try to turn any negatives into positives. We should hopefully be in a better position tomorrow after the changes we made for today, and I'm hopeful that the race will be stronger."
With Vettel enjoying a pre-eminent position at Ferrari, having won two of the first three races and scored twice as many points as his team mate, there is a risk of Raikkonen 'riding shotgun' and holding up rivals as the German gets away.
Raikkonen, the 2007 world champion, has not been on the podium since July last year and Saturday was the first time the Finn had qualified on the front row since Ferrari's home Italian Grand Prix in September 2015.
Read the full article on eurosport.co.uk: Just one of those weekends, says Hamilton