The alleged complicity of Bhalla's wife in the Noida land scam has queered the pitch for his elevation.
Official sources said Kalam had written to the Prime Minister's Office following recommendations of Bhalla's appointment by a three-member Supreme Court collegium comprising senior judges.
The President also took into account the dissenting note of one of the three judges of the collegium against Bhalla's appointment, the sources said.
Government is bound by the recommendation of the collegium if the same name is recommended again after reconsideration. There is, however, no time frame for the Government to act on the recommendations.
Lok Sabha Speaker Somnath Chatterjee and Chairman of Rajya Sabha Bhairon Singh Shekhawat had also received some representations made by eminent lawyer Shanti Bushan against Bhalla's elevation.
Chatterjee also wrote a letter to Law Minister Hans Raj Bhardwaj and apprised him of the complaints besides seeking an early response from his office on the issue.
"On hearing from you, I shall decide whether the matter shall be taken up by me with the leaders of different political parties for action, if any." The Lok Sabha speaker said in his letter.
When contacted Shanti Bhushan told PTI that on behalf of the Committee of Judicial Accountability, he had written letters to Kalam, Shekhawat, Prime Minister Manmohan Singh and the Lok Sabha Speaker opposing Bhalla's elevation.
Bhushan alleged that Bhalla's wife Renu had purchased 7,200 square metres of land in Noida from "land mafia" for a paltry sum of Rs 5 lakh.
Though the Additional District Magistrate had submitted a detailed report to District Magistrate on the "shady" deal, no action had been taken, the noted lawyer alleged.
The former Law Minister said that he had only received a response from the Vice President and Chatterjee saying that the complaint had been forwarded to Chief Justice of India and the Law Minister.