Victoria Atkins, who is the Louth and Horncastle MP, is married to British Sugar managing director Paul Kenward.
Ms Atkins said she would recuse herself from some government business if necessary.
The Department of Health and Social Care said Ms Atkins had declared all her outside interests.
"Anyone who knows me knows that I am very, very independently minded," Ms Atkins said.
"I voted enthusiastically for the sugar tax when that came before Parliament."
Before becoming health secretary in the Prime Minister's reshuffle on Monday, Ms Atkins had previously been financial secretary to the Treasury.
It is not the first time Ms Atkins has been challenged over her husband's business interests.
In 2018, when she was a drugs minister she wasaccused of "hypocrisy"over British Sugar's licence to produce a non-psychoactive variant of the cannabis plant.
The Home Office stated the MP had declared the interest and had recused herself voluntarily from "policy or decisions relating to cannabis, including licensing".
Ms Atkins said: "I have always been scrupulous in ensuring that those interests are declared and that I recuse myself from any such decisions.
"Not because I think I am at risk of being in any way influenced but I am very conscious of the perception of that."
The secretary of state said she had a "complicated relationship" with sugar as a type 1 diabetic.
"I am focused on ensuring the health of our country," she said.
"I want to work with our healthcare professionals both in the NHS and in social care and that is how we are going to tackle some of these very big public health issues."
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The new health secretary has insisted there is no conflict of interest with her husband's senior role in the British sugar industry.