Rod Houston says the Highland League will be guided by the SFA and Scottish Government with the season set to continue.
Earlier this week First Minister Nicola Sturgeon announced lockdown measures in Scotland for the rest of this month.
Despite the tightening of restrictions, football has been allowed to continue for the time being.
In Scotland, the Premiership is the only league where Covid-19 testing of players and staff is required.
As a result, questions have been asked in some quarters as to why the likes of the Highland is being allowed to carry on.
League secretary Houston said: “This is not a debate of absolutes – it’s about judgement calls.
“All along we have taken advice from the Scottish FA and through them the Scottish Government.
“The current advice is to continue, the minute that advice changes we will take stock.
“We are subject to that level of governance and we don’t have an issue with it.
“We feel we have been kept well-informed throughout the whole year, we feel we have been well-advised throughout the whole year and we will continue to use those good offices to ensure we do what is best.”
It has taken a huge amount of work at all levels of football to allow the game to return in some form during the coronavirus pandemic.
Things have been no different in the Highland League and, having started the 2020-21 season, Houston believes clubs are keen to continue.
He added: “There are people at each and every club who have put in a lot of hard work to ensure the facilities are suitable and the appropriate processes are in place.
“That has been a massive undertaking by all Highland League clubs.
“It has taken a lot of work and commitment to get football back, albeit behind closed doors.
“I suspect they are not inclined to lose the benefit of that work by stopping just now unless circumstances dictate.”
When the 2020-21 Highland League season kicked off on November 28, some clubs – the 10 in the Highlands and Moray – were able to play in front of a limited number of supporters.
Mainland Scotland being moved into Tier 4 on Boxing Day has meant all teams have been operating behind closed doors since.
Despite that Houston feels the response to the return of the Highland League has been positive.
He said: “The overall response has been very positive and they have been delighted to get back to doing it.
“I completely understand people who are not directly involved wondering about it, which is why we’re subject to the governance we are.
“It’s not a case of we think we’re right and others are wrong – the balance of judgements right now is to continue playing, which is not a decision based on absolutes.”