Turkey's move follows a breakdown in ties and rising violence in its southern neighbour.
Turkishs Economy Minister Zafer Çağlayan also said Damascus had started allowing Turkish trucks to enter Syria on Tuesday after blocking their entry last week in retaliation for sanctions imposed by Ankara.
Turkey has been eyeing new trade routes to the Middle East ever since relations with Syria broke down following Ankara's increased criticism of President Bashar al-Assad over his bloody crackdown on a popular uprising that began in March.
"It is very easy for us to bypass Syria but we had preferred not to do this. We had still wanted to transit our trade through Syria and let the Syrian economy make money out of this," Çağlayan told Turkish television channel CNBC-e.
"But they wanted it this way. I say again, whatever they do they will suffer more than Turkey every time. To do trade with the Middle East and the Gulf, (we) do not have to go through Syria. Our A, B and C plans are already ready."
Çağlayan said cargo ships would start travelling between Turkey's southern Mediterranean port of Mersin and Egypt's Alexandria on Thursday. Trucks would also begin crossing into Iraq.
Last week, Turkey announced a list of economic sanctions on Syria it said would target the government, including freezing state assets and imposing a travel ban on senior officials as well as suspending financial transactions.
Syria responded over the weekend by suspending a free trade agreement between the two countries and by imposing a 30 percent tariff on all Turkish imports and prohibitive duties on fuel and freight. Turkey shrugged off the decision saying the Syrian people would be the ones that suffered most.
Çağlayan said Damascus had started blocking Turkish trucks from crossing into Syria last week in retaliation for Ankara's sanctions but begun allowing them to cross again on Tuesday after Turkey decided to pursue alternative routes.
"As soon as we started implementing steps (to open new routes) yesterday evening, the Syrian government immediately started allowing our trucks to pass," he said.
Turkey is a major trading partner for Syria with bilateral trade last year totalling some $2.5 billion. Syria received more than 10 percent of its imports from Turkey in 2010 while imports from Syria made up only 0.3 percent of Turkey's total imports, Çağlayan said this week.
On Nov. 17, Çağlayan said while exports to Syria had risen by nearly 4 percent in the first nine months of 2011, October and November figures had shown a 10 percent drop compared to last year as the increasing violence put off Turkish firms.
Muslim Turkey was once one of Syria's closest regional allies, and Turkey's Prime Minister Tayyip Erdogan had built a strong rapport with Assad.
But as the violence grew worse and Assad ignored Erdogan's advice to halt a crackdown on protesters and make urgent reforms, relations became increasingly frosty and Erdogan has now bluntly told Assad he should quit.
Turkey now hosts Syrian military defectors and an umbrella Syrian opposition group.