The four-day ministerial meeting which began in Singapore on Saturday ended Tuesday.
International Trade and Industry Minister Datuk Seri Mustapa Mohamed said the areas of concern include Bumiputera issues, government procurements, environment, labour, intellectual property rights and state-owned enterprises.
In the area of goods market access, Mustapa said Malaysia was prepared to undertake comprehensive commitments "but this would depend on the overall balance of the negotiations."
"Malaysia has thus far made good progress in the bilateral discussions on market access," he said in a statement in Kuala Lumpur.
On tobacco, Mustapa said Malaysian officials have convened informal consultations with officials from a number of countries to pursue an exception from the TPP for tobacco and tobacco products.
"Overall, there are still a lot of work that remains to be undertaken by the negotiators.
"Negotiators will be consulting on a suitable time-table to continue work with a view to find a solution to the remaining issues," he said.
Mustapa said Malaysia would continue to undertake domestic engagements with various stakeholders to share with them the outcome of the Singapore meeting and the way forward.
He said the meeting was preceded by a technical-level discussions at the chief negotiators level on the various outstanding issues.
"The aim of the ministerial meeting is to consider the possible options and explore compromises on the outstanding issues from the December 2013 meeting. The intensive four-day meeting focused on market access and text," he said.
Mustapa said the ministers made progress on a number of outstanding issues but significant gaps remained in the more difficult areas such as intellectual property rights, state-owned enterprises and the environment.
In these areas, the ministers decided on options for negotiators to work on to find the appropriate compromises, he said.
In the area of market access, the ministers exchanged information on the 'state of play' in the various bilateral negotiations.
"This is an important area which remains outstanding. The ministers discussed the viable options in moving forward negotiations in the area of market access and further bilateral negotiations will continue," he said.
Meanwhile, speaking at a media conference in Singapore, Mustapa said Malaysia was pleased with the outcome of the meeting although there was no "landing zones" yet.
"No agreement yet, but at least there is some way forward. We are going to look at all the areas of concern and if they are fundamental to our policies or our laws, it's difficult for us to compromise," he said after the meeting ended.