Ibrahim Kalin also signalled that recent tensions between Turkey and the United States may be easing as Washington has become more "careful" in its support for Syrian Kurdish YPG fighters.
A "cessation of hostilities" agreement in Syria is due to take effect at midnight (2200 GMT on Friday). But the Syrian branch of al Qaeda, which like other jihadist groups is not covered by the accord, has called for an escalation in fighting against President Bashar al-Assad's government and its allies.
"We support this ceasefire in principle, but unfortunately we have serious concerns about the future of this ceasefire as the fighting goes on," Kalin told a news conference.
Under the deal, which has not been signed by Syria's warring parties themselves and is less binding than a formal ceasefire, the government and its enemies are expected to stop shooting so that aid can reach civilians and peace talks begin.
The Assad government and its Russian allies say they will not halt strikes targeting jihadist groups such as Islamic State and the al Qaeda-linked Nusra Front. Other rebels seen as moderates by the West say they fear this stance will be used to justify attacks on them too.
NATO member Turkey's role in the ceasefire has been complicated by its deep distrust of the Washington-backed Syrian Kurdish YPG. Ankara sees the group as a terrorist organisation and has shelled YPG positions in northern Syria in recent weeks in retaliation, it says, for cross-border fire.
Change in US
Washington, which says the YPG is not a terrorist organisation, has supported the group in the fight against
Islamic State in Syria.
However, Kalin said on Friday: "I see some change in the US position. I think they are being more careful. They have also raised concerns about the YPG's moves and connections with the Russians and the Assad regime."
YPG forces have exploited recent gains by forces loyal to Assad, backed by Russian airstrikes, and seized additional territory near Turkey's border.
Washington has called on the YPG to stop seeking additional territory and Ankara to stop shelling YPG positions.
The YPG told Reuters this week it would respect a ceasefire but reserved the right to respond if attacked. Kalin said Turkey would respond to any incidents threatening its national security by applying its rules of engagement.
Kalin also said Saudi planes - due to take part in air strikes against Islamic State - had started arriving at Turkey's Incirlik air base.
Turkish crackdown
An independent Turkish broadcaster has been pulled off the air over allegations of "spreading terrorist propaganda," adding to fears the government is cracking down on the media.
Turkey's satellite provider Turksat halted broadcasts of IMC TV at the request of an Ankara prosecutor investigating whether the channel supported a "terrorist" group.
The plug was pulled on IMC mid-broadcast during a live interview with Can Dundar and Erdem Gul, two prominent journalists who were freed pending trial after spending 92 days in prison.
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