Fernando Alonso brought some welcome cheer to Ferrari after a troubled week, by posting the second fastest lap in the afternoon after leading the first session.
Championship leader Nico Rosberg was third fastest in his Mercedes followed by the Red Bulls of Daniel Ricciardo and Sebastian Vettel in fourth and fifth respectively.
It was a mixed day for Ferrari and their new team principal Marco Mattiacci, who was installed after Stefano Domenicali dramatically quit on Monday.
Hamilton clocked 1min 38.315sec on the quicker soft tyre compound, despite complaining of understeer into turn one.
The Englishman lost almost an hour of track time over the two 90-minute Friday practice sessions as his engineers worked on trying to improve his problematic front suspension which had left him languishing in eighth place in the first session.
Late in the session Hamilton, despite being quickest, again got on the radio to complain: "Something's not right with this car."
Felipe Massa demonstrated that his Williams was improving by being sixth fastest with a lap of 1min 39.118sec.
In the morning on the medium compound tyres Alonso had clocked 1min 39.783sec to lead the pack with championship leader Nico Rosberg in the Mercedes second, 0.398sec behind.
After a chilly morning with temperatures in Shanghai hovering around the 13 degrees Celsius mark, temperatures rose slightly to 16C for the second free practice at the 5.451 kilometre Shanghai International Circuit.
The cool conditions meant many drivers suffered from lack of heat in their tyres and struggled with braking throughout the two sessions.
Force India, second in the constructors championship after Sergio Perez and Nico Hulkenberg came third and fifth respectively in Bahrain, had a poor day by their season's high standards so far.
Hulkenberg was 11th with a best lap of 1:39.736 and Perez back in 15th with 1:40.124.
Pastor Maldonado in the Lotus had a torrid day. In the first session he spun while fiddling with his steering wheel.
"I crashed," he exclaimed over team radio. "Oh OK," came the reply. "I'm sorry," added Maldonado, sheepishly.
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