The response from President Benigno Aquino's spokesman Edwin Lacierda came after the Global Times newspaper - with close ties to the ruling Communist Party - featured an editorial yesterday saying it was "laughable" imagining Philippine personnel "stumbling after US forces".
"We don't understand where this insecurity of the Chinese towards us is coming from. Where do we have the wherewithal to compete against China as a superpower?" Lacierda said.
He said the exercises were more than just wargames and have shown their benefits through the US assistance provided after Super Typhoon Haiyan struck in 2013, leaving at least 7,350 people dead or missing.
"China wants to make their own comments. That's their opinion. But we are not bound by their opinion and we certainly do not agree with how they described us," he added.
Lacierda dismissed calls to engage China in bilateral talks, saying other countries were also involved in the dispute.
The Philippines has also said Chinese ships recently used water cannon to drive Filipino fishermen away from a disputed shoal - just 220 kilometres from one of the sites of the 10-day wargames.
Aside from improving defence ties with the United States, the Philippines has been seeking greater US military aid in the face of Chinese "aggressiveness" in disputed waters.
China claims sovereignty over most of the South China Sea, including areas just off the coasts of other Asian nations, using vague demarcation lines that first appeared on Chinese maps in the 1940s.