The number of deaths appears to be going up while the total without shelter has fallen by a fifth, Leo Varadkar added.
He pointed to an increase in State outreach efforts over recent times.
It is going in the right direction but it is not enough
He said: “For every five people you have homeless there are now four. It is going in the right direction but it is not enough.”
Mr Varadkar said bed capacity is being increased along with enhanced outreach to bring rough sleepers in from the cold this winter.
The Fine Gael leader added: “There has been an increase in the number of people using the services suffering premature death last year.
“The number of deaths is rising at a time when the number (of homeless) is falling. We need to get to the bottom of that.”
Sinn Féin housing spokesman Eoin Ó Broin said addictions, suicide, mental health problems and hypothermia were amongst the reasons for deaths.
He told the Dáil: “Their deaths are indeed a tragedy.”
He urged the Government to increase funding for mental health care and to provide thousands of extra beds.
The Department of Housing has published its latest homelessness figures for the month of September.
They show there were 8,656 people accessing homeless services in Ireland over the month, including 2,583 children.
Ironic, they say beds are left empty.
— Cllr. Anthony Flynn (@AnthonyICHH) November 25, 2020
The numbers decreased slightly, by 46, in September compared to the previous month.
The number of families accessing emergency accommodation has shown a small increase, up by eight to 1,128.
Bodies of two homeless men found in Dublin
Budget 2021 makes provision for €218 million in funding for homeless services next year.
The original budget allocation for 2020 was €166 million, but it was increased by €30 million in July to €196 million.
Homeless charity Focus Ireland has welcomed the decrease in the figures for September but has called for the moratorium on evictions during Level 5 restrictions to be increased.