Le Hoai Anh, the chairwoman of Hal Group, a company in Ho Chi Minh City that distributes and sells European cosmetics, said she worried about trade disruptions or punitive measures that might lead to higher import tariffs.

“We don’t know exactly how it will be,” she said of Vietnam’s trading relationship with Europe. “But we are expecting a bad situation.”

The German Foreign Office said in an email that the Vietnam trade deal would need to win approval in both the German and European parliaments, and that members of both bodies clearly saw the political implications of Mr. Thanh’s disappearance.

Vietnam’s Foreign Ministry did not respond to emailed questions.

The deal is the European Union’s second effort at a trade pact in Southeast Asia, after one with Singapore that is nearing ratification. The largest benefits for the E.U. would be in Germany, which last year imported $8 billion in goods from Vietnam — including footwear, textiles, coffee and seafood — and sold it $2.3 billion in machinery, equipment, motor vehicles, chemicals and other products. The deal would also create arbitration mechanisms aimed at giving European manufacturers, many of them German, more legal security here.

For Vietnam, the upshot would be private-sector growth in an economy that has long been top-heavy with state-owned enterprises and overdependent on development aid. Beneficiaries would likely include companies in both established export industries, such as fisheries and textiles, and also in emerging ones like scooters, smartphones and furniture.

Mr. Thanh, 51, had been a senior official in the southern province of Hau Giang and the chairman of PetroVietnam Construction, a subsidiary of the state oil giant PetroVietnam. He was accused of mismanagement that resulted in losses of about $147 million.