Hamilton went into qualifying for the Bahrain Grand Prix knowing he would face a five-place grid penalty for a gearbox change.
That had been necessary after a left-rear tyre blowout at the end of final practice that forced him to take defensive action to avoid a high-speed crash.
The 28-year-old managed to limp back to the pits, but with damaged suspension it led to repairs to the left-rear of the car, with one of the knock-on effects being the requirement of a new gearbox.
It is understood Hamilton collected debris that led to the puncture, an unavoidable incident for which he theoretically should not have been punished.
It means Hamilton, after qualifying fourth behind suprise polesitter in team-mate Nico Rosberg, will now line up ninth and facing a tough battle to make it three successive podium finishes.
Suggested to Brawn it was time for the regulation to be addressed, he replied: "I think Lewis would agree with you because he made the very same point to me, that external influences have given him a penalty.
"The difficulty we have in the future is where we get marginal cases where you have a problem, perhaps aggravated by the driver, and you don't get a gearbox failure as such, but it needs to be changed.
"Then you get into these long debates.
"But it is frustrating to get a penalty when there has been an outside influence. It's annoying.
"Fortunately it doesn't happen too often, but if it were to happen at a critical part of the season then it would be doubly frustrating, so it's worth looking at again."
Hamilton cut a bitterly unhappy figure post race as he knows such an incident undoubtedly affects his early title hopes, with the Briton currently 12 points adrift of Red Bull's Sebastian Vettel.
Asked for his thoughts on a potential rule change, Hamilton said: "It doesn't really matter. The rules are the rules.
"I've got a penalty and I will have to suck it up and deal with it. I just got unlucky as I think it was some debris with the tyre."
Pirelli motorsport director Paul Hembery was certainly dismissing any prospect one of his company's tyres lay behind Hamilton's woes.
Hembery said: "The problem seen on Lewis' Mercedes during free practice was not the result of a structural tyre failure, but instead must have been down to a piece of debris on the track."
It was one of those bitter-sweet afternoons for Mercedes in light of Rosberg helping them to back-to-back poles for the first time since their return to F1 three years ago, and after Hamilton led away the field a week ago in China.
With two DNFs in his first three races, Rosberg has so far suffered in contrast to Hamilton, but was smiling again after claiming what is only his second pole in his 132 races.
"This is great for me because the start (to the season) has really not gone to plan, with a lot of issues," said Rosberg.
"I'm really hoping this is going to kickstart my season. It's the first time everything has really gone to plan. Up until now it has been great.
"To turn up with the pole position, which I have to admit is a bit of a surprise, I'm really, really happy with.
"I'm now looking forward to tomorrow [Sunday] when hopefully everything will go well, although I'm not sure we have what it takes to win the race."
That is based on the fact this year's Mercedes, whilst quick over one lap, lacks the race pace of rivals Ferrari, Red Bull, and Lotus on occasion.
Rosberg can certainly expect to come under attack at the start as reigning triple world champion Vettel lines up alongside him on the front row, with Fernando Alonso directly behind from third.
With Mark Webber facing a three-place penalty of his own following a collision with Toro Rosso's Jean-Eric Vergne in Shanghai, it means Ferrari's Felipe Massa moves up to fourth in the absence of Hamilton and the Australian.
Force India duo Paul Di Resta and Adrian Sutil occupy the third row, with Lotus' Kimi Raikkonen eighth following a difficult qualifying for the Finn who trails Vettel in the standings by three points.
Jenson Button managed to creep into the top 10 shoot-out, and will start 10th as that was as good as his McLaren would allow, with team -mate Sergio Perez 12th.
As for Marussia's Max Chilton, who celebrates his 22nd birthday on Sunday, he was slowest in qualifying for the first time this year.
Chilton, though, will not be last on the grid as that spot belongs to the Sauber of Esteban Gutierrez who also has a five-place grid penalty after running into the back of Sutil in China.
Alonso declared himself "very, very happy with third".
It is the third successive race Alonso will start from third, adding: "Normally we struggle a lot in qualifying, so this has put us in a strong position for the race."