"We also have to take the prison's viewpoint, whether or not such visits could result in bad implications towards the prison", he told reporters after the Home Ministry's monthly assembly here.
Dr Mahathir, who is now the chairman for the opposition Pakatan Harapan (PH) coalition, on Wednesday expressed his disappointment at not being allowed to visit Anwar, with hospital officials telling the former premier that they had received instructions not to allow him in.
Anwar is serving a five-year sentence for sodomy and is in hospital after undergoing surgery on his right shoulder in November.
Zulkifli also said that not all applications will be approved as the department has to give careful consideration to each case.
"My visit to see Datuk Seri Anwar was disallowed".
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He said the prohibition was not a ministerial order, instead it was subject to the discretion of the Prisons authorities.
"They (prisons department personnel) only said that they have received orders from someone high, which means the Minister of Home Affairs that I'm not allowed to see Anwar", Mahathir said.
"According to Section 26 of the Prisons Act, when a prisoner is in a hospital, it is still like he is in prison".
He added that visitation is granted to non-family members only if there is a "pressing or important matter". "However, other visitors require special permission".
Dr Mahathir yesterday was barred from meeting Anwar at the Cheras rehabilitation centre after staff told him that there were orders from above not to allow him in.
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The UMNO Treasurer said it appeared unusual that before this Dr Mahathir had absolutely no interest in visiting Anwar in prison.
That meeting led to the thaw in tense ties between the two leaders.
Dr Mahathir is now chairman of the four-party opposition alliance Pakatan Harapan, and Anwar its de-facto chief.
The visit was supposed to be Dr Mahathir's first visit to the Parti Keadilan Rakyat (PKR) leader after the former was picked to be PH's prime minister if the opposition coalition wins the coming general election, which is expected to be called in the next few months.
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