Twice in recent weeks Hamilton has been the subject of remarks from Ecclestone, with the latest revelation one that should arguably have been kept private between them.
It has put Hamilton in an awkward position, as Ecclestone has made it clear Red Bull was the 28-year-old's first-choice destination in his bid to escape McLaren after 13 years.
However, Red Bull owner Dietrich Mateschitz's loyalty to Mark Webber closed the door for Hamilton who instead turned to Mercedes, although his initial reaction was dismissive when mentioned by Ecclestone.
It has all left Hamilton far from impressed with Ecclestone, given the relationship he has previously enjoyed with the 82-year-old.
"I'm not really quite sure why Bernie keeps making comments about me. He only makes comments about me," said Hamilton, speaking to Press Association Sport.
"It makes me a little bit nervous because we have quite a good relationship. Through respect I'm quite open with him about a lot of stuff.
"The situation is I said to my management team to speak to all the teams and to give me what the best options were. There was no particular one team I was pushing for more.
"At the end of the day I chose to be here, I'm happy and it's the best decision I've ever made."
That decision saw Hamilton on the podium in Sunday's Malaysian Grand Prix behind a controversial Red Bull one-two as Sebastian Vettel disregarded team orders to claim the win.
Hamilton, however, was embarrassed to be there, as he has made it clear team-mate Nico Rosberg should have been standing in his place given the German's pace in the closing stages.
Rosberg, though, was twice ordered to file in behind Hamilton, with the latter appreciating how hard that must have been for his friend.
"It is very difficult because we all exist, work and train hard to win, to move forward and beat the people who are ahead of us," said Hamilton.
"So for someone to help the team like that is absolutely a positive, but then Nico and I have a great history.
"He has always been very mature, is a long-standing part of this team who love and have the utmost respect for him. He deserved it more."
Hamilton has made clear that come a time when the roles are reversed and he is told to hold station, then he will "absolutely" obey the order.
For now, with Hamilton and Rosberg third and fourth in Malaysia, and harassing the Red Bulls for a long period of time, that has fuelled the former's belief a win is definitely now on the cards this year.
"If we look at the positives we are the second quickest team, which is a massive bonus," added Hamilton.
"To be in a position where I was competing with the Red Bulls at some points in the race is a great feeling.
"We're not the quickest, but if we keep working in the direction we're going then there is the possibility we could be the quickest this year."