Law Minister Ravi Shankar Prasad said in the Rajya Sabha that the letter was written on August 3 but did not give details.
The fresh letter was sent after the Supreme Court collegium did not accept some suggestions for the MoP while agreeing to some others, he said.
"The government, after careful consideration of the matter, has sent its response to the Chief Justice of India vide letter dated August 3, 2016," Prasad said.
The minister maintained that the government is making efforts to supplement the existing MoP by making the appointment process transparent, fair and accountable within the parameters set by various supreme court judgements and at the same time ensuring independence of judiciary.
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Prasad said the additional judges whose tenures were ending were given three months' extension as per the apex court order while the validity of the National Judicial Appointments Commission Act is being heard by the Supreme Court.
Prasad said the process of appointment of judges has been resumed as the process of finalisation of MoP is likely to take some time.
"During 2016, 100 additional judges have been made permanent and 52 fresh appointment of judges have been made," he said.
"Proposals for appointments have been received from High Courts from February 2016 ownwards," he said, adding three Supreme Court judges have also been appointed.
The whole process as per MoP takes six months as states/ intelligence bureau and Supreme Court collegium are consulted and then the case is processed for approval, Prasad said.
Noting that there are huge vacancies in courts, he said unless these vacancies are filled, it would be difficult to take up the pending cases.
Tankha said the systems of fast track courts, ad-hoc judges and Gram Nyayalya (rural courts) are not functioning.
Participating in the debate, Satish Chandra Misra (BSP)
said there has been a stalemate in appointment of judges. He sought to know the total number of vacancies that have been created during this period.
He said there is no judge from Scheduled Castes in the Allahabad High Court and asked "How many judges are from Scheduled Castes in Supreme Court and High Courts?"
Naresh Agrawal (SP) asked whether there would be reservation in the appointment of judges in the Supreme Court and High Courts. He also wanted to know whether reservation issue is there in the MoP, which is currently being finalised.
K Keshava Rao (TRS) said there should be adequate representation of Telangana in the appointment of judges for Andhra Pradesh High Court.
Shukla said the accountability of judges should be fixed and they should also be brought under RTI.
He also quipped that lawyers should not become Law Minister, an apparent reference to Prasad.
D Raja (CPI) said Indian judiciary continues to have "class-bias and caste-bias" and is "not free from corruption".
Referring to cases related to dalit massacres in Andhra Pradesh and Bihar, he said the accused were acquitted by the High Courts after being convicted by lower courts.
Sukhendu Sekhar Roy (TMC) said the entire system of appointment of judges has come to a standstill. He also asked the minister why members of the Upper House should not discuss if MoP is being finalised.
Earlier, Law Minister had told the House that he would not speak on anything related to MoP as the matter is under discussion. To this, Deputy Chairman P J Kurien said he was free not to answer any question.