Lee had taken the first set but struggled in the second before quitting in the third with cramps, with Malaysian media claiming that the air conditioning had been switched off midway through the match to aid Lin.
The BWF, after queries from the BAM, said they had contacted the local organising committee (LOC) and had been assured there was no foul play.
"The LOC confirmed that the air-conditioners in the venue were not turned off at any time during the finals," the BWF said in a statement carried by Malaysia media.
"However, due to the increase in the number of spectators on the final day - particularly during the men's singles match - the temperature went up and the venue became hotter."
Malaysian daily newspaper The Star quoted one source saying temperatures rose to 32 Celsius (90 Fahrenheit) at the indoor venue.
The BWF's explanation did little to appease BAM secretary Ng Chin Chai.
"We wanted the BWF to investigate. Now, we have been enlightened by the statement from the organisers," he was quoted as saying by The Star.
"I was present at the stadium and I find it hard to accept their explanation."
(Reporting by Patrick Johnston in Singapore; Editing by John O'Brien)
