By Agence France-Presse
China has alarmed and angered its neighbours by claiming dominion over most of the South China Sea and building a string of artificial islands and military airbases.
But the outspoken Duterte -- keen to court trade and investment from Beijing -- has mostly withheld criticism.
In a change of tone, Duterte said in a speech late Tuesday to business entrepreneurs that China had no right to claim airspace above man-made islands.
Philippine officials have claimed military pilots are repeatedly warned off by Beijing as their planes approach Philippine-held Thitu island, which lies beside a Chinese air base built on top of Subi Reef.
"You cannot create an island. It's man-made and you say that the air above this artificial island is yours," Duterte said, according to a transcript released by the presidential palace Wednesday.
"That is wrong because those waters are what (one) would consider international sea. And the right of innocent passage is guaranteed," said Duterte, who did not refer to any specific incident.
He added that he did not want to "quarrel" with China.
The comments follow allegations in May of Chinese harassment of Filipino troops at another South China Sea garrison.
Duterte's national security adviser Hermogenes Esperon told reporters at the time that the Philippines could go to war "if our people are hurt there".
There was no immediate response from the Chinese embassy in Manila.
In May China landed several combat aircraft -- including the long-range, nuclear-capable H-6K -- at another island airfield in the sea for the first time, triggering international concern.
Despite this, it has denied militarising the area, through which roughly a third of all global maritime trade passes.
An international maritime tribunal ruled early in Duterte's presidency in 2016 that China's claims to the area have no legal basis.
The Philippines is a military ally of the US, which says it is not taking sides in the various South China Sea territorial disputes.
However, the US navy has forcefully asserted its right to freedom of navigation in the area, repeatedly sailing close to the man-made islands and drawing Chinese protests.
Brunei, Malaysia, Taiwan and Vietnam also have claims in the sea.