According to latest data, less than half of the member states, 13 countries in total, have completed their legislative processes.
These include Germany, Italy, Sweden and the Czech Republic.
Among those yet to complete implementation are the UK, Spain, Poland and Ireland.
The deadline for implementation is 20 May.
The law is an update of the 2001 tobacco directive. Its main aim is to make tobacco products less attractive to young people.
The legislation will make it mandatory for all cigarette packs to carry picture warnings covering 65 per cent of their surface. eCigarettes will be regulated, either as medicinal products, if they claim to help smokers to quit, or as tobacco products.
The legislation bans flavourings in cigarettes and roll-your-own tobacco that would make the product more attractive by giving it a 'characterising flavour'. Menthol is banned from 2020.
Member states have to put the provisions on tobacco products into effect within two years of the updated directive's date of entry into force this Friday.
Axel Gietz, of Imperial Tobacco, which markets a range of cigarettes, says the delay has is "causing uncertainty for everyone from consumers to regulators."
Speaking at a news conference in Brussels on Tuesday, he said this had left regulators, manufacturers and consumers in "legal limbo."
He said, "While the delays in some countries create legal uncertainty for everyone, in Imperial Tobacco. We are very much on track to be ready to comply with the new rules".
Gietz continued: "We have been preparing for the change for years and are actively engaging with the authorities to be able to adapt to the changes in the different countries as soon as they are known."
He said he has faith that more countries will comply around the deadline and that regulators will continue to maintain dialogue on how best to deal with any delays to implementation.
Further comment came from Alan Hardacre, also from Imperial Tobacco, who said, "We are as always open to dialogue with regulators on how to best to deal with delayed implementation that we are left with in some countries. We firmly believe regulation is developed better when all concerned parties are involved in the process."
The directive was adopted by the European Parliament in April 2014.
Its passage was marked by an intense battle with considerable activity from traditional tobacco lobbyists and electronic cigarette firms, as well as from NGOs working on public health.
If not all countries meet the deadline, it may create legal uncertainty for both the regulators as well as for companies.
"This is not least the case when uncertainty exists as to exactly what the national legislations will look like or when they will enter into force," warned Hardacre.