The Chancellor announced a pilot of payments for new childminders with more for those who sign through agencies.
Akshata Murty was listed as a shareholder in one of those agencies, Koru Kids, as recently as 6 March.
The prime minister's press secretary said all Mr Sunak's interests "have been declared in the usual way".
Ministers are expected to provide a written list of all financial interests that might "give rise to a conflict".
Mr Sunak mentions Ms Murthy's venture capital company, Catamaran Ventures, in his list of ministerial interests, but does not mention Koru Kids.
The PM also did not mention Ms Murthy's links to Koru Kids when he was questioned by MPs over the policy at a parliamentary committee hearing on Tuesday.
Labour MP Catherine McKinnell asked Mr Sunak whether he had any interest to declare, and in reply he said: "No, all my disclosures are declared in the normal way."
The Liberal Democrats say there are "are serious questions for Rishi Sunak to answer" about "any extra income his family could receive from his own government's policy", and have urged the government's ethics adviser, Sir Laurie Magnus, to investigate Mr Sunak over a potential breach of ministerial rules.
Labour's deputy leader Angela Rayner said Mr Sunak must explain why his wife's shareholding "was not deemed necessary to publish in the register of members' interests"."He must urgently correct the record and set out what steps he took to avoid an actual or perceived conflict of interest," Ms Rayner said.
When asked about Ms Murty's shareholding - which was reported by the i newspaper - Mr Sunak's press secretary told reporters the details of Ms Murthy's holding in the agency were not in the public domain, but indicated they would be included in the updated statement of ministers' interests, due out in May.
"The ministerial code sets out a process by which ministers declare their interests. They do that in writing, in this case to the Cabinet Secretary. That process was followed to the letter by the prime minister," the press secretary said.
Declarations to the Cabinet Office are not immediately available to MPs or others to see.
Pressed that MPs are usually expected to draw attention to an interest they have declared if questioned about it in a committee, Mr Sunak's press secretary said "there was not a specific interest that was put to him".
The BBC has sought to ask both the company and Ms Murthy for comment.
The pilot of bonuses for childminders was announced in the Budget on 15 March as part of the government's overhaul of childcare.
Mr Hunt said the government would be "piloting incentive payments of £600 for childminders who sign up to the profession, rising to £1,200 for those who join through an agency".
The pilot could drive up the number of childminders entering the profession and generate more business for companies such as Koru Kids.
Koru Kids is listed as one of six childminder agencies on the government's website.
On its website, Koru Kids welcomed the government's reforms and said "the new incentives open to childminders are great".
The website says new childminders would get a bonus of £1,200 if they "come through an agency like Koru Kids who offer community, training and ongoing support".