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Almost Moore digraphs appear in the context of the degree/diameter problem as a class of extremal directed graphs, in the sense that their order is one less than the unattainable Moore bound $M(d,k)=1+d+\cdots +d^k$, where $d>1$ and $k>1$ denote the maximum out-degree and diameter, respectively. So far, the problem of their existence has only been solved when $d=2,3$ or $k=2$. In this paper, we prove that almost Moore digraphs of diameter $k=3$ do not exist for any degree $d$. The enumeration of almost Moore digraphs of degree $d$ and diameter $k=3$ turns out to be equivalent to the search of binary matrices $A$ fulfilling that $AJ=dJ$ and $I+A+A^2+A^3=J+P$, where $J$ denotes the all-one matrix and $P$ is a permutation matrix. We use spectral techniques in order to show that such equation has no $(0,1)$-matrix solutions. More precisely, we obtain the factorization in ${\Bbb Q}[x]$ of the characteristic polynomial of $A$, in terms of the cycle structure of $P$, we compute the trace of $A$ and we derive a contradiction on some algebraic multiplicities of the eigenvalues of $A$. In order to get the factorization of $\det(xI-A)$ we determine when the polynomials $F_n(x)=\Phi_n(1+x+x^2+x^3)$ are irreducible in ${\Bbb Q}[x]$, where $\Phi_n(x)$ denotes the $n$-th cyclotomic polynomial, since in such case they become 'big pieces' of $\det(xI-A)$. By using concepts and techniques from algebraic number theory, we prove that $F_n(x)$ is always irreducible in ${\Bbb Q}[x]$, unless $n=1,10$. So, by combining tools from matrix and number theory we have been able to solve a problem of graph theory.