Yitzhak Molcho was on Sunday and Monday questioned by police along with David Shimron, a relative of Netanyahu and his family lawyer who also represented German industrial giant ThyssenKrupp in Israel.
Authorities released their identities on Tuesday.
Molcho, a lawyer who partners with Shimron and is also a relative of the Netanyahus, announced last month that he would step down from his position as Netanyahu's envoy in February next year.
Police refused to divulge why Molcho was questioned, saying merely it was part of the submarine affair, but media said he was suspected of having used his position to advance the deal.
More From This Section
Last month, Germany signed a deal to sell three Dolphin submarines from ThyssenKrupp to the Israeli navy.
Negotiations on the sale had been frozen for three months due to concern in Berlin over the corruption investigation in Israel.
Shimron has already been detained for questioning over the affair.
Netanyahu himself has not been named as a suspect in the submarine case.
He is however being investigated in two separate graft probes and is expected to be interrogated again in the coming days.
The two other probes involving Netanyahu centre on the premier allegedly receiving luxury gifts from wealthy supporters and suspicions he sought a secret deal for favourable coverage with the publisher of top-selling daily Yediot Aharonot.