"We have some problems of success," he told a post-Cabinet lekgotla media briefing.
Ports were unable to handle the growth in imports and exports, and the railway system was struggling with increased freight movement.
The Cabinet deliberated the matter, and came to the conclusion that large investment was needed in railways and harbours, Mbeki said.
A document issued at the briefing stated the government would provide additional resources to improve Transnet's rail network.
More money would be put into easing congestion at the Durban, Cape Town and Port Elizabeth ports.
The country's road programme would also receive more resources, accompanied by a phased reduction in axle mass limits on the roads, the document stated.
Other plans included an "investment upgrade" in high-traffic border posts.
Mbeki said skills shortages was another result of economic growth and modernisation. The new economy demanded a "different kind" of worker.
To this end, cabinet decided on interventions like the recruitment of scarce skills from outside the country, as well as setting aside a portion of the National Student Financial Aid Scheme and National Skills Fund to train scientists, researchers, managers, engineers and artisans.
There would also be a new focus on making sure the Sectoral Education and Training Authority system functioned properly, and on giving public servants skills training.
Mbeki said last week's lekgotla sought to measure progress in reconstruction and development made in the past year, as well as the past nine years under democratic government.
The feeling was that much has been achieved, and that the country was now in a better position than ever before to deal with the outstanding issues, he said.
While it was important to continue improving the delivery of social services, there should also be a new focus on changing communities to help them develop themselves.
Many of the poorest would remain marginalised despite continued economic growth, the president said - hence the importance of sustainable rural development and urban renewal programmes.
Rural areas were mostly unable to attract private capital, and the State had a responsibility in that regard.
Mbeki said attempts should be made, for example, to attract nurses and teachers to rural areas by paying them some incentive.
"It is not only a matter of provision of services and creation of jobs, but also a change of societies so they can become viable economic entities".
This would be one of the aims of the extended Public Works Programme.
Turning to calls for a basic income grant, Mbeki said this was not a viable option. The social security system was already extensive and included old-age pensions, disability grants, child support and unemployment insurance.
"Giving everybody R100 is not going to make any difference," the president said.
"You and me, who don't need it, would be taking the money away from somebody who does. It would make no sense". – Sapa.
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