Hamilton completed 25 laps of the 5.4 km Shanghai International Circuit in the afternoon session to end the day with a best time of one minute 38.315 seconds, edging out the morning's pacesetter Fernando Alonso by a tenth of a second.
Formula One world championship leader Nico Rosberg in the other Mercedes was third, the German falling four tenths of a second short of his team mate's benchmark.
Despite ending the day fastest, Friday's two practice sessions were far from trouble-free for Hamilton, who arrives in China having won the last two races and is gunning for his first grand prix hat-trick.
The Briton was limited to running nine laps in the morning after a suspension issue brought an early end to his session.
The problem persisted into the second 90-minute session and Hamilton was forced to miss out on the opening half-hour of the post-lunch action as his team worked to fix his car.
Once out on track, Hamilton continued to experience problems with his car's handling and at one point radioed his team to tell them there was "something wrong with this car.
"It was quite a difficult day today as we missed some of this morning's session which put us on the back foot slightly, but we were glad to get some laps in the second session at least," Hamilton said after practice.
"We're not too happy with the balance of the car at the moment, so we need to go and work on that," the 2008 world champion added.
Hamilton's Mercedes team have set the standard this season, the German marque having swept to three dominant wins in as many races.
However, the Brackley-based team did not seem to have as big an edge over the opposition as in Bahrain two weeks ago, though they could well have been masking their true pace.
Fernando Alonso in particular - being closely watched by his new boss Marco Mattiacci - looked strong in his Ferrari.
Having set the pace in the morning, the Spaniard swapped the fastest time with Rosberg's Mercedes for most of the afternoon before teams switched their focus to high-fuel long runs.
"We have brought some small updates here, which we already tried at the Bahrain test," Alonso said after practice.
"Everything worked well and that's good news. Leaving aside the performance of the others, I am happy with what we have done today," he added.
His team mate Kimi Raikkonen, however, was hampered by technical glitches and forced to sit out the first session.
But the Finn bounced back in the afternoon, racking up 25 laps on his way to the seventh-fastest time.
Behind the top three, Daniel Ricciardo, who was third in the morning, continued to lead the charge for world champions Red Bull.
The Australian ended the day fourth ahead of team mate Sebastian Vettel on what Germany's four-time world champion said was a good day for the team.
However, he conceded that the Milton Keynes outfit was not yet a match for the top teams.
Felipe Massa in the Williams followed the two Red Bulls in sixth, ahead of Raikkonen and McLaren's Jenson Button.
Romain Grosjean gave Lotus, who have endured a trying start to the year, cause for optimism by setting the ninth-fastest time, while Russian rookie Daniil Kvyat rounded out the top 10.
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