The administration had said earlier the magnitude 3.4 quake detected at 0829 GMT was a "suspected explosion".
The quake also caps a week in which President Trump and North Korea leader Kim Jong Un exchanged increasingly bellicose insults and follows a threat on Thursday by the North to carry out a significantly more risky nuclear test.
South Korea's weather agency said it was analyzing the nature of the quake and its initial view was that it was a natural earthquake.
An official of South Korea's Meteorological Agency said acoustic waves should be detected in the event of a man-made natural disaster.
There was no immediate reaction from China's Foreign Ministry.
North Korea this month carried out an underground test on a hydrogen bomb estimated to be 16 times the size of the U.S. bomb that destroyed Hiroshima in 1945. The last test registered as a 6.3 magnitude quake.
The area where the quake struck is not known to experience natural earthquakes.
The U.S. Geological Survey said it could not conclusively confirm whether the quake, which it measured at magnitude 3.5, was man-made or natural.
The news agency issued a fresh report later, saying the seismic service after further study concluded the quake was natural and not the result of a nuclear test.
Tensions have continued to rise around the Korean peninsula since Pyongyang carried out its sixth nuclear test, prompting a new round of United Nations sanctions.
President Trump and North Korean leader Kim Jong Un spent the past week trading insults and ratcheting up the already-high tension between the countries.
In his first address to the world gathering on Tuesday, US President Donald Trump threatened to "totally destroy North Korea".
The sources said lenders were asked to fully implement United Nations sanctions against North Korea and were warned of the economic losses and reputational risks if they did not do so.
The U.S. put its own sanctions on North Korea on Thursday, against banks or companies doing business with the country.
Saturday's seismic activity came on the same day China announced it would limit trade with the North, reducing its fuel exports to its neighbor and banning all textile imports.
The president assured those in attendance, without details, that he would defend the USA against any offensives launched by North Korea: "I can tell you one thing, you are protected, OK?"