The seven-time F1 champion managed just 20 laps across the two practice sessions at a track he last visited in 2005 during his F3 days.
After 37 minutes were lost in FP1 following a power unit issue on Sebastian Vettel's Aston Martin that raised safety concerns, Hamilton suffered his own PU problem after just five minutes of FP2 that forced him to pull off track.
That was to the delight of the tens of thousands of Max Verstappen fans who let out a roar when they saw Hamilton was out of the session.
With the trouble believed to be related to the oil system, Hamilton said: "I just lost the power, they told me to stop. It's not the end of the world.
"This morning I only got 20 minutes of running with the red flag, so naturally it puts on the back foot."
The good news for Hamilton is the PU was the oldest in the pool and so will likely be swapped out for the second, with the latest that was introduced last weekend at Spa saved for next week's power track of Monza.
Bottas "had a good session" - Hamilton
Team-mate Bottas, however, enjoyed trouble-free running, with Hamilton indicating he will be turning to the Finn for information on car set up.
"Valtteri looks like he had a good session, so hopefully tomorrow we can try and make up for some of the time we lost," added Hamilton.
"I made some changes into the [second] session but I only got one lap with it so it's very hard to pick the good or bad points from that change.
"But as I've said we've Valtteri who did a lot of running, lots of data analysis from the long runs, most other people got their long runs, so we'll see how it goes."
Despite the limited amount of track action, Hamilton could not help but express his delight at F1's return to Zandvoort after a 36-year absence, since when significant changes have been made, including the construction of two banked corners.
"The track is epic," added Hamilton. "It's really fantastic. It brought back so many memories of when I first got out there, from when I was driving here.
"I knew it was great when I was in Formula 3 but it's crazy in a Formula 1 car. The speed we're going through turn seven, it's a real racing circuit.
"It will be interesting but I don't think you will be overtaking because it is such high, high downforce and super-fast corners you probably won't be able to follow through.
"But let's hope there's a good strategy for Sunday."
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