"To be honest, I had never imagined I will regain the world number one spot after the doping issue," Lee, who returned to action in May last year after a backdated eight-month doping ban, told Bernama news agency.
"My target was top four, nothing more. However, being the number one will further inspire me to keep going," he said.
Chen, however, can wrest the top ranking back if he wins the ongoing Australian Open, which Lee skipped because of an injury.
Lee lost the last two Olympic singles finals to great rival Lin Dan of China but remains optimistic he can become Malaysia's first Olympic gold medallist.
"My confidence was back after beating Lin Dan and Cheng Long in their own backyard during the China Open and again at the Asian Championships," added Lee, who has won two of Malaysia's three silver medals in the country's Olympic history.
"Before the ban, I had been the world number one for 199 weeks. After the doping issue, I knew I had to work hard knowing it would not be an easy task but I am glad that I managed to do it, what more at this age.
"I want to use the remaining two plus months to focus and train for the Olympics. I have to be physically and mentally fit because this will be my final Olympics."
(Reporting by Amlan Chakraborty in New Delhi; Editing by John O'Brien)
