Mr Martin said the unilateral action on the Brexit divorce agreement corrodes trust.
Mr Martin said the Withdrawal Agreement contains mechanisms designed to deal with issues that arise.
He made the comments during an online address to the Brookings Institution in Washington, for a series of virtual events in the lead-up to St Patrick’s Day on Wednesday.
Mr Martin said: “The decision of the United Kingdom to leave the European Union created a whole new category of challenges that we have had to deal with in recent years.
“Our shared membership of the EU had helped to create the context in which the Good Friday Agreement was secured. Changing that context removed an important prop.
“We worked hard to minimise and to mitigate its worst impacts, not least the risk of the return of a hard border to the island of Ireland.
“In this, we had strong backing from our partners in the EU, but also, critically, from our friends in the US. As a result, the Withdrawal Agreement between the EU and the UK includes a special protocol on Ireland and Northern Ireland to address the unique circumstances of the island.
“The protocol is specifically designed to protect the Good Friday Agreement, and the achievements of the peace process. Crucially, it avoids a hard border on the island of Ireland.
“It is the only agreed and viable means available to do so.”
The Fianna Fail leader said the protocol also protects the all-island economy and Ireland’s place in the single market.
He said it helps minimise and mitigate the worst impacts of Brexit, but warned it cannot completely remove them.
“The UK has decided to leave not only the EU, but also its single market and customs union, and that means increased trade friction,” Mr Martin added.
“What we are now seeing – the increased need for checks and controls; the form-filling and bureaucracy – is a direct consequence of that choice.
“Where we can find pragmatic ways to minimise that friction, within the framework of the protocol, the EU is ready to do so.
“I do not for a moment dismiss genuinely held difficulties and concerns, and I will support EU engagement with the UK to find agreed ways forward, where we can.
“In fact, the Withdrawal Agreement contains within it mechanisms specifically designed to deal with issues that arise – a Joint Committee and specialised committees.
“That is where teething problems should be worked through, so that we can find common solutions.
“Unilateral action to disapply or not to implement aspects of the protocol does nothing but corrode trust, the only basis on which sustainable long-term solutions can be found.
“It exacerbates uncertainty and instability, two things Northern Ireland can well do without.”
Ireland’s Foreign Affairs Minister Simon Coveney said the decision by the European Commission to take legal action was “not a welcome development”, but the approach of the UK Government had left no alternative.
“Unilaterally changing how Protocol is implemented is breach of agreement,” Mr Coveney tweeted.
“We need to get back to UK/EU cooperation, working with business in NI and focused on solving problems together.”