Briefing members of Parliament's public service and administration portfolio committee, performance monitoring and evaluation department director general Sean Phillips also warned it was unlikely government would meet its 2014 national employment target.
He said rural unemployment had now risen to a point where over half of those living in rural regions, defined by Statistics South Africa as "tribal areas", were unemployed.
"We are not doing well in terms of our target to increase rural employment … There has been an alarming rise in rural unemployment."
Phillips said rural unemployment had risen from 44% in 2009 to 52% this year.
This rise could be attributed to the country's slow rate of national economic growth, inadequate progress regarding small-holder farmer development and a lack of growth in employment in the commercial agriculture sector.
On general employment in the country, he said it was "unlikely" that the 2014 target of improving the percentage of people at work – to an employment rate of 45% – would be met.
"The latest measurement … is at 41% which is the same as it was in 2009."
The employment rate is the percentage of the labour force actually employed.
Phillips also said there was little progress on youth unemployment.
"We haven't made good progress with regards to our commitment to reduce youth unemployment. There is an urgent need for decisions to be made on interventions in this regard."
Against a backdrop of continuing service delivery protests around the country, he also told parliamentarians at least two key 2014 targets – provision of sanitation and electricity – would not be met.
According to a document handed to members at the briefing, which deals with government's performance and the problems it faces, access to sanitation increased from 77% in 2009 to 82% in 2011.
"[But it is] not on target for 100% in 2014," it states.
A Cabinet lekgotla last week made providing sanitation a national priority project.
On access to electricity, the briefing document says this is "not on target for 100% in 2014, due to a lack of generation capacity, lack of bulk infrastructure, and distribution networks".
Referring to his department's "midterm review of the priorities of government", tabled in March this year, Phillips said this document recognised that the 2009 recession had dealt a big setback to efforts to reduce unemployment in South Africa.
He warned that the effects of the recession were continuing.
"This has not left us, and there is a real risk it will continue, and that global growth will be slower [this year] than it was [last year].
This would make many of the country's economic and job creation targets difficult to attain, he said.
His remarks come a day after the latest Reserve Bank Quarterly Bulletin show South Africa's current account deficit has widened dramatically.
According to reports, the deficit – the shortfall between revenue from exports and the import bill – rose to 6.4% of GDP from 4.9% in the first quarter of this financial year.
Phillips said inequality in South Africa also remained a big problem.
"We also haven't made good progress yet in reducing the Gini coefficient and the share of the poorest 40% in total income, due to the … impact of the global crisis."
There had also been "insufficient progress with regard to implementation of policies to reduce inequality, such as improving basic education and small business development".
According to the mid-term review, government is hoping to reduce South Africa's Gini co-efficient – an international scale on which the country ranks as one of the world's most unequal – from 0.70 to 0.59 by 2014.
On Tuesday this week, former ANC Youth League leader Julius Malema called on mineworkers to participate in "a five-day strike every month" until their demands for higher wages are met. – Sapa