The team have used orders tactically before but this was the first time Mercedes have employed instructions that reversed positions to ensure a win for one driver over another.
"We have only had team orders in that one race", Hamilton told reporters in Japan.
"I don't think there's much sense in that".
"I'm definitively still allowed to win but it will all depend on the situation", said the Finn.
"Well, within a week you can't do too many things differently, so we hope that the track suits us a bit better and we have a better weekend than in Russia", the four-time Formula One champion said, reports Efe news.
Lewis Hamilton had a lot of sympathy for Bottas as well as he was seen consoling his teammate after the race and at the podium.
Mercedes said the decision was necessary due to Hamilton coming under pressure from title rival Sebastian Vettel and the fact he had damaged his rear tyres overtaking the Ferrari on track earlier in the race.
"I've been really happy when I look back at these races, I couldn't have hoped for better performances", he said. How, with 125 points still to play for, has this happened to the German driver and his team which have had a superior auto for most of the season? I can not fight for the championship anymore, Lewis is, I'm a team player and I'm willing to help.
This week the series is in Suzuka, where Hamilton has won three of the last four Japanese Grand Prix.
"As far as I am aware, when I drive down the straight I'm not allowed to move twice - but there are drivers that do move twice and nothing happens to them. Winning is everything, but that time will come later". Being in third I knew that I'd be losing several points to Sebastian, which through my driving wasn't supposed to happen so I was very eager to get by.
Hamilton has established a strong lead, winning five of the past six races but many have been against the head with Ferrari having the stronger vehicle.
Ferrari team boss Maurizio Arrivabene likened the sweeping, high-speed Suzuka circuit to Silverstone, the British Grand Prix venue where then-championship leader Vettel won in July. "We're a strong team, we want to win both world championships and we work together, as a team, to do that".
"I think I've said many times that we have a strong vehicle, but I don't think, against the people's opinions, that we had a dominant auto at any point this year", said Vettel.
"We haven't lost direction".
"We know that one mistake or one DNF that could disappear quite quickly, so we want to make it [the gap] as big as we can". You never know where you are in comparison to the others, but I'm pretty sure by speaking to all our engineers that we are where we wanted to be.
It is a position the German team have enjoyed for most of the season yet once again they are taking nothing for granted.