"I doubt there is a real danger of that happening," the Japan Football Association (JFA) told Reuters amid signs of an end to the stand-off.
"It's in the hands of the lawyers but it shouldn't come to a boycott."
The JFA has opposed demands by Japan's players association (PFA) for a pay rise, pointing to the two million yen ($24,500) paid to each player for wins at last year's World Cup in South Africa.
That figure was double the amount the JFA shelled out at the 2006 tournament in Germany.
The PFA's demands began before the Blue Samurai won the Asian Cup in Qatar in January but they have softened their stance in recent days, asking for talks with the JFA.
JFA chief Junji Ogura launched a withering attack on the PFA, accusing them of "losing the plot" by threatening to jeopardise home games against Montenegro and New Zealand in March.
"This is not what the PFA is there for," the 72-year-old told Japan's Sankei Sports newspaper.
"We paid the players bonuses for winning the Asian Cup, despite the fact there was no prize money.
"They get paid by their clubs, and they get offers from foreign clubs. That's the value of playing for your national team."
Japan's players are calling for an increase in win bonuses and a share of the revenue from their own image rights.
Japanese internationals currently receive an estimated 100,000 to 200,000 yen for every match they win, but are asking for a minimum of one million yen.
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