Sports Minister Sarbananda Sonowal, however, said it will "examine the possibility of recommending" the name of the Olympic bronze-medallist for the award.
Saina had expressed disappointment at the Sports Ministry deciding to reject her application for the prestigious Padma Bhushan this year but Sonowal sought to put the record straight, saying that his ministry received the letter of nomination late.
"I have seen reports in sections of the media that Sports Ministry didn't recommend the name of Ms Saina Nehwal for the Padma Bhushan award. On ascertaining the facts, I have come to know that Sports Ministry had not received any nomination from the Badminton Association of India prior to January 3, 2015," Sonowal said in a statement.
"A packet containing a letter, dated August 9, 2014, nominating Ms Nehwal for the Padma Bhushan award was received by the staff at my residence on January 3, 2015," he said.
Sonowal, however, said that despite the late receipt of her application, his ministry would examine tomorrow the possibility of recommending her name to the Home Ministry for the award.
"I would also like to categorically state that Ms Saina Nehwal has made every Indian proud and I sincerely hope she will continue to bring laurels to Indian sports," he said.
"I would like to assure everyone that my ministry would examine the possibility of recommending her name separately," he said.
Badminton Association of India(BAI) on its part said it had sent the letter of nomination in August last year and it has got the acknowledgment of receipt from the sports ministry.
"We had sent the recommendation on August 9 and we also received an acknowledgment for the same from Sport Ministry. I don't know what is the confusion. In fact, when Saina had called the officials of the ministry, initially they said they haven't received the letter but later said it is there but
they didn't consider," BAI President Akhilesh Das Gupta said.
"I think Saina is a deserving candidate and she needs to be considered for the Padma Bhushan, or else it will be an injustice to her," he added.