South Korean media on Monday warned of a "Trump risk" threatening the alliance between Washington and Seoul amid high tensions over the North's weapons ambitions.
The two countries are bound by a defence pact and 28,500 US troops are stationed in the South.
But the new US president has said in recent interviews that Seoul should pay for a "billion-dollar" US missile defence system being deployed in the South to guard against threats from the nuclear-armed North.
He has also pushed for renegotiation of what he called a "horrible" bilateral free trade pact that went into effect five years ago, calling it an "unacceptable... deal made by Hillary".
The remarks stunned Seoul, with South Korean politicians immediately rejecting his push for payment for the Terminal High Altitude Area Defense (THAAD) battery.
Tensions are high over the North's nuclear and missile programmes -- it has ambitions to develop a rocket that can deliver a warhead to the US mainland -- and threats on both sides have raised fears of conflict.
"Trump's mouth rattling Korea-US alliance" said a front-page headline in South Korea's top-selling Chosun daily on Monday.
"There are issues that are far more important than just money," it said in an editorial.
"If either country keeps reducing the alliance to the matter of money or the economy, it is bound to undermine basic trust."
Seoul, it said, needed to come up with "various Plan Bs" for the future.
The THAAD system is being installed at a former golf course in the South.
This has infuriated China, which sees it as compromising its own capabilities and has responded with a series of measures seen as economic retaliation, even as Washington looks to Beijing to rein in Pyongyang.
Trump told CBS on Sunday that if the North carried out a sixth nuclear test he "would not be happy".
"And I can tell you also, I don't believe that the president of China, who is a very respected man, will be happy either," Trump said.
"We'll see" whether that signified military action, said Trump, who also described the North's leader Kim Jong-Un as a "pretty smart cookie".
- 'Pain and backlash' -
Over the weekend Seoul's presidential office said US National Security Advisor H.R. McMaster had appeared to backtrack on THAAD, telling his South Korean counterpart by phone that the US would bear the cost of the missile deployment as initially agreed.
But McMaster told Fox News Sunday that the "last thing" he would ever do was contradict the president, and that "the relationship on THAAD, on our defence relationship going forward, will be renegotiated as it's going to be with all of our allies".
Another major South Korean newspaper, JoongAng Ilbo, accused Trump's administration of sending "confusing and contradictory messages", creating a "chaotic situation" that dealt a "huge blow" to the bilateral alliance.
"The US must be well aware of the pain and backlash Seoul has endured to push for the THAAD deployment," it added.
Asked in the Fox News interview about the possibility of mass casualties in South Korea the event of conflict -- Seoul is within range of the North's conventional artillery -- McMaster responded: "What the president has first and foremost on his mind is to protect the American people."
Another major daily, Dong-A Ilbo, declared on its front page Monday: "Trump Risk... we need to come up with new strategy for Korea-US alliance".
The US president was pouring "a barrage of verbal bombs" on Seoul in a challenge to its next leader, who will be elected on May 9.
"We hope that Trump will be more careful with his words," it said in an editorial. "Who's going to smile if our alliance is shaken? It will be North Korea's Kim Jong-Un and China's Xi Jinping."