John Sopko, special inspector general for Afghan reconstruction, found that project "planning, co-ordination and execution" was weak.
Security costs were likely to rise in the short-term, it added, as private companies hand over to Afghan forces.
The US plans to withdraw its troops from Afghanistan by the end of 2014.
The quarterly report released on Monday also found that several construction projects were so far behind schedule that they were unlikely to be up and running before US troops leave the country.
It said "a significant portion" of the US government's $400m (£254m) investment in large-scale infrastructure projects in fiscal year 2011 alone may have been wasted because of the poor planning.
The report also says the US Army has accepted contract construction that was so poor it prevented multi-million dollar police bases from being used.
The inspector general noted that one base was unoccupied because it has no viable water supply.
The report continues: "Other deficiencies included leaking fuel lines, unconnected drain pipes, poorly built guard towers, and improperly installed heating and ventilation systems."
The inspector general said there was still time to improve the outcomes of the projects in Afghanistan, but warned that time was running out.
"The US reconstruction program has been an essential component of the US strategy in Afghanistan to defeat al-Qaeda and ensure that terrorists cannot operate from Afghan territory," the report says.
The report notes that if Congress approves President Barack Obama's latest budget request the US will have allocated almost $100bn on Afghan reconstruction.
The inspector general notes that the US has never provided so much funding over a similar period of time rebuilding another country.
He points out that reconstruction aid to Germany in the aftermath of World War II amounted to less than $35bn in 2011 dollars.
The report pledges "aggressive oversight of these extraordinary funds" to save taxpayer money and improve the outcomes of the projects.
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