John Pullinger said the commission was not just "a body of the UK Parliament", and would have an "independent discussion" with Scottish officials if they wanted "something to be done that helps them with their democracy".
His remarks, published in the Daily Telegraph, put the commission on a collision course with the Prime Minister, who says he will reject a request for an "irresponsible and reckless" second referendum.
Nicola Sturgeon has said that May's Holyrood elections gave the SNP a mandate for a second poll, and there have been suggestions the Scottish Government may seek a unilateral poll if Westminster rejects a demand for a section 30 order.
Asked whether such a poll could take place if Mr Johnson refused the request, Mr Pullinger said: "That is what I've read."
He added: "The UK Electoral Commission is also the electoral commission specifically for Scotland and Wales. We have a direct reporting line to Scotland and Wales. And, as of April this year, we are directly funded by Scotland and Wales too.
"If the Parliament in Scotland is wanting something to be done that helps them with their democracy, we will have an independent discussion with them about whether it's appropriate for the commission to support that."
Michael Gove said earlier this week he “can’t see” Mr Johnson granting a new Scottish independence referendum before the next general election in 2024.