"We are planning to have our certificates ready in April together with our partner Guardtime," said Kalle Killar, undersecretary for e-health and innovation at the ministry.
Killar said the digital certificates would help people both for travelling and in their everyday life and would be both easier to verify and more secure than paper ones.
He added that a global vaccination certificate which the Estonian government is working on with the World Health Organization (WHO) would likely take years to develop.
Estonia, a tech-savvy Baltic state that has served as a testing ground for innovations, has one of the highest coronavirus infection rates in Europe.
Its prime minister, Kaja Kallas, is currently in quarantine after testing positive for the coronavirus.
The EU member of 1.3 million people also has one of the highest vaccination rates in Europe.
The European Union has announced plans for digital vaccination certificates before the summer to facilitate travel.
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