Islam visited the Dhanmondi residence of Home Minister Asaduzzaman Khan Kamal around 10pm on Monday.
Asked why he met the Hifazat leaders, the minister said: "The Hifazat leaders don't want mass arrests."
"But I told them there were no mass arrests. Only those involved in crimes are being held.”
Several people were killed after protests and strikes called by Hifazat in objection to Indian Prime Minister Narendra Modi's visit last month sparked violence in Dhaka, Narayanganj, Brahmanbaria and Chattogram.
A number of top Hifazat leaders have recently been arrested in connection with various old cases following the incident.
On the meeting with the home minister, Hifazat leader Maulana Ataullah Amin said, "The secretary general has met the minister to highlight the overall situation in the country."
But the group will not issue a statement on the matter, he added.
Asked if the Hifazat leaders have discussed any other issues, Kamal said, “They spoke about opening the madrasa in Kamrangirchar. But no other issues were discussed."
Meanwhile, in the face of the police crackdown, Babunagari released a video message on Monday, urging leaders and activists of Hifazat not to engage in any kind of violence or vandalism.